apraga/org - Change NCBHHUESPLBDQI2VOWF74N3KMHS6MOSWQPSYBISHOTN2JQLSVLYQC

Paper idea, archiving old tasks

Created by Alexis Praga on November 18, 2023

NCBHHUESPLBDQI2VOWF74N3KMHS6MOSWQPSYBISHOTN2JQLSVLYQC

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In channels

main

Change contents

Insertion in workout.org at line 6878 [4.1]

[3.494]

* <2023-11-16 Thu> Gymnastics
- Cheval d'arçon : 3/4 tour !
- Barre asymétrique : "enroulement" arrière ok (mais style à travailler)
- Trampoline : travail salto à hauteur maximale

Replacement in projects.org at line 69 [4.123895]

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B:BD[5.654] → [3.509:541]

*** TODO Demander pour ouverture de ligne
    SCHEDULED: <2023-11-16 Thu>

[5.612]

[5.686]

*** WAIT Demander pour ouverture de ligne
    SCHEDULED: <2023-11-20 Mon>

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SCHEDULED: <2023-11-13 Mon>
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SCHEDULED: <2023-11-20 Mon>
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** DONE Cas clinique H.influenza :hinfluenzae:
CLOSED: [2023-09-28 Thu 11:43]
:PROPERTIES:
:CATEGORY: bacterio
:END:
*** DONE Finir bibliographie H. influenza
CLOSED: [2023-09-09 Sat 20:19] SCHEDULED: <2023-09-09 Sat>
/Entered on/ [2023-09-09 Sat 16:40]
*** DONE Envoyer biblio initiale à Xavier
CLOSED: [2023-09-10 Sun 22:51] SCHEDULED: <2023-09-10 Sun>
*** DONE Résumé article PCR
CLOSED: [2023-09-28 Thu 11:43]
/Entered on/ [2023-09-17 Sun 16:08]
*** DONE Envoyer première version à Xavier
CLOSED: [2023-09-17 Sun 22:31] SCHEDULED: <2023-09-17 Sun>
/Entered on/ [2023-09-17 Sun 16:08]
** DONE Examen bactério :partiel:
CLOSED: [2023-10-18 Wed 22:52]
:PROPERTIES:
:CATEGORY: bacterio
:END:
*** DONE Passe 1: tous [37/37]
CLOSED: [2023-10-05 Thu 16:58] DEADLINE: <2023-10-06 Fri> SCHEDULED: <2023-10-06 Fri>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire)>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [X] <(EBCU etiologies)>
  - [X] <(ECBU interpretation)>
  - [X] <(ECBU pre-analytique)>
  - [X] <(EEQ, CIQ)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Hygiène)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes )>
  - [X] <(Pre-analytique bacteriologie)>
  - [X] <(Qualité)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Securite Transfusionnelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [X] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [X] <(Vaccination personnel)>
  - [X]  https://scut.srht.site/notes/medecine/20230528235124-culture.html
  - [X] A. agalactiae
*** DONE Passe 2: cours non tobmé avec interro + révision + interro [33/35]
CLOSED: [2023-10-15 Sun 12:59] DEADLINE: <2023-10-11 Wed> SCHEDULED: <2023-10-07 Sat>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [-] Mécanisme résistance antibio
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire)>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [X] <(EBCU etiologies)>
  - [X] <(ECBU interpretation)>
  - [X] <(ECBU pre-analytique)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes)>
  - [X] <(Pre-analytique bacteriologie)>
  - [-] BMR (cours ? définition a minima)
  - [X] <(Qualite)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [X] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [X] <(Culture)>
  - [X] A. agalactiae
*** DONE Passe 3 [27/36]
CLOSED: [2023-10-18 Wed 00:10] DEADLINE: <2023-10-16 Mon> SCHEDULED: <2023-10-22 Sun>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [ ] Mécanisme résistance antibio
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire )>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [ ] <(EBCU etiologies)>
  - [ ] <(ECBU interpretation)>
  - [ ] <(ECBU pre-analytique)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes)>
  - [X] <(Pre-analytique bacteriologie)>
  - [ ] BMR (cours ? définition a minima)
  - [X] <(Qualite)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [ ] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [ ] <(Culture)>
  - [ ] A. agalactiae
  - [ ] Bactérie (refaire un tour)
** DONE Présentation dépistage hémato :presentation:
CLOSED: [2023-10-19 Thu 18:29]
:PROPERTIES:
:CATEGORY: bacterio
:END:
*** DONE Refaire analyse bouche
CLOSED: [2023-10-07 Sat 17:49] SCHEDULED: <2023-10-07 Sat>
*** DONE Traitement patients bouches
CLOSED: [2023-10-07 Sat 18:01] SCHEDULED: <2023-10-07 Sat>
*** DONE Faire analyse selles
CLOSED: [2023-10-07 Sat 19:30] SCHEDULED: <2023-10-07 Sat>
:LOGBOOK:
CLOCK: [2023-10-07 Sat 18:02]--[2023-10-07 Sat 19:30] =>  1:28
:END:
*** DONE Revoir avec Audrey pour différence (bleu et jaune)
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
*** DONE Réunion audrey
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
*** DONE Traitement patients selles
CLOSED: [2023-10-10 Tue 22:52] SCHEDULED: <2023-10-09 Mon>
*** DONE [#A] Résumer Torres 2022
CLOSED: [2023-10-08 Sun 12:42] SCHEDULED: <2023-10-07 Sat>
<[Pdf]> - "~/papers/bacterio/torres2022.pdf"
<[Notes]> - "~/roam/research/biblio.org#** Multi-body-site colonization screening cultures for predicting multi-drug resistant Gram-negative and Gram-positive bacteremia in hematological patients"
*** DONE Première version avec contexte, Torres et nos résultats
CLOSED: [2023-10-11 Wed 21:47] SCHEDULED: <2023-10-08 Sun>
"~/roam/research/presentations/bacterio/depistage hemato/notes.org#* Présentation"
*** KILL Présenter Santibiez 2023
CLOSED: [2023-10-19 Thu 18:29]
*** DONE Corriger présentation
CLOSED: [2023-10-17 Tue 23:19] SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 22:01]

Replacement in projects.org at line 79 [4.123895]
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```
SCHEDULED: <2023-11-11 Sat>
```
[31.44]
[32.106]
```
SCHEDULED: <2023-11-25 Sat>
```

Replacement in projects.org at line 81 [4.123895]

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** DONE Déclaration stage hémato UNESS
CLOSED: [2023-11-14 Tue 22:21] SCHEDULED: <2023-11-13 Mon>

[32.142]

[33.14]

*** DONE CVEC
CLOSED: [2023-11-18 Sat 11:43]
*** TODO UFR santé: mail envoyé car inscription impossible
SCHEDULED: <2023-11-22 Wed>

Deletion in projects.org at line 86 [4.123895]

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∅:D[34.399] → [33.94:130]

B:BD[33.94] → [33.94:130]

** DONE Envoyer devis dentiste à mutuelle
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 12:18]

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∅:D[17.1844] → [20.522:659]

B:BD[16.3458] → [20.522:659]

B:BD[20.659] → [5.1223:1309]

B:BD[5.1309] → [32.212:241]

*** DONE Mail Juliette + Paul pour resoumission
CLOSED: [2023-09-10 Sun 22:36] SCHEDULED: <2023-09-10 Sun>
/Entered on/ [2023-09-10 Sun 22:21]
*** DONE Mail Dr Laithier
CLOSED: [2023-09-18 Mon 19:36] SCHEDULED: <2023-09-17 Sun>
/Entered on/ [2023-09-17 Sun 16:06]
*** DONE Avis paul sur ACPA non
CLOSED: [2023-10-02 Mon 21:58]
*** DONE Corriger article
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-05 Sun>
**** DONE Ajouter images Dr Vidaud
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
**** DONE Comprendre score LRR pour gain
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-21 Thu>
**** DONE Corriger discussion: remaniement complexe
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
**** DONE Phénotype "mild" chez le père + détailler moléculaire
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
**** DONE Traitement FBXW7 ?
CLOSED: [2023-10-11 Wed 16:08] SCHEDULED: <2023-10-15 Sun>
Lié à NF1 et non FBXW7 (voir mail V. Laithier)
*** DONE Réponse reviewer
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
*** WAIT Correction Juliette

[35.23689]

[32.241]

*** TODO Implémenter corrections

Replacement in projects.org at line 384 [4.123895]

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∅:D[36.1101] → [42.1021:1022]

B:BD[42.1021] → [42.1021:1022]

B:BD[42.1022] → [36.1102:1182]

** Article thèse
*** Idée
Framework pour tester des pipeline d'exome
1. Les outils pour télécharger les données de comparaison (pipeline(s) nextflow) :  GIAB +/- chm
2. Les outils pour comparer les VCF: package nix pour hap.py
3. les données brutes pour lancer le pipeline et comparer ensuite (GIAB)
   NB: pipeline existant si on télécharge depuis SRA...
4. les outils pour génerer des données de synthèse : xamscissors (SNV seulement), bamsurgeon
5. des données de référence
Motivation: pas d'article qui centralise tout avec une solution "clé en main".

[41.111]

[43.11816]

** Article thèse :bisonex:
[[id:feaee0cd-8bf7-45bb-851c-9e590e984985][Idées article]]

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B:BD[20.793] → [32.270:298]

** DONE Remplacer clavier SK :clavier:
CLOSED: [2023-10-28 Sat 21:36]
/Entered on/ [2023-10-07 Sat 22:58]
*** DONE Demande à Cooler Master un remplacement
CLOSED: [2023-10-15 Sun 12:43] SCHEDULED: <2023-10-15 Sun>
Envoyée <2023-10-07 Sat>
Sera probablement refusée car via Amazon
*** DONE Retour Amazon
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-28 Sat>
Renvoie vers le constructeur ...
** DONE Coudre fermeture éclair pantalon
CLOSED: [2023-10-11 Wed 12:48] SCHEDULED: <2023-10-11 Wed>
/Entered on/ [2023-10-09 Mon 22:09]
** WAIT certificat de baptême
SCHEDULED: <2023-11-13 Mon>

[44.2233]

[20.821]

** TODO certificat de baptême
SCHEDULED: <2023-11-20 Mon>

Replacement in projects.org at line 650 [4.123895]

B:BD[20.900] → [13.427:530]

∅:D[13.530] → [30.418:648]

∅:D[24.993] → [30.418:648]

B:BD[30.418] → [30.418:648]

B:BD[30.648] → [13.531:607]

∅:D[13.607] → [30.693:1161]

B:BD[30.693] → [30.693:1161]

B:BD[30.1161] → [38.314:398]

∅:D[38.398] → [27.407:443]

B:BD[27.407] → [27.407:443]

** DONE Réclamation train Paris - Besancon
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-22 Sun>
/Entered on/ [2023-10-16 Mon 22:01]
*** KILL TER
CLOSED: [2023-10-16 Mon 22:05]
"Par ailleurs, en cas de retard ou de suppression de train, il n'existe pas de garantie ponctualité sur TER, aucun remboursement ne sera effectué."
*** DONE Allianz
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-23 Mon>
Manque justificatif de retard mais le site ne trouve pas le trajet...
https://www.ter.sncf.com/bourgogne-franche-comte/services-contacts/bulletin-retard-resultats?search=N4IgJgpgDghgTgFwK5wgZQQeygBQDYwDGEIAXKAHYwC2JpIO8AlgM4C0AQhHIQJ4AEHTCgDmmERQj82-Rrxb8wAcgCCSAG7cJJADQhWGbPiJ0EcJBD1MwZEAA4A7ADY7Ttw5B6EvKHRAALViw4JkIQAF89eBD1GDxDXAJiMkoaPy4WGAoAc8wKNgA1JkwEBF19FgTjZNIzCysbekcHAEY7AAZ2jy8fP0CWYNCIqLgYuIARGDLbACZ2mYBmNhb25YBWABVO0m3OgGp5nfbPEGimWLwNplpbFqdSABYPcKA
** DONE Rendre livres BU
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-27 Fri>
/Entered on/ [2023-10-27 Fri 21:14]

[20.900]

[45.1513]

*** TODO Appeler
SCHEDULED: <2023-11-20 Mon>
*** TODO Demander à Aurélien
SCHEDULED: <2023-11-21 Tue>

Deletion in projects.org at line 662 [4.123895]

B:BD[46.63] → [47.14:123]

∅:D[48.42] → [49.553:606]

∅:D[50.71] → [49.553:606]

∅:D[51.71] → [49.553:606]

∅:D[47.123] → [49.553:606]

∅:D[52.128] → [49.553:606]

∅:D[53.485] → [49.553:606]

B:BD[49.553] → [49.553:606]

B:BD[49.606] → [54.433:560]

B:BD[54.560] → [55.14:249]

B:BD[55.249] → [14.4685:4767]

B:BD[14.4767] → [16.3546:3643]

B:BD[16.3643] → [13.608:718]

∅:D[13.718] → [16.3722:3741]

∅:D[30.1190] → [16.3722:3741]

B:BD[16.3722] → [16.3722:3741]

*** DONE Changer courroie distribution :courroie:
CLOSED: [2023-09-30 Sat 18:53] SCHEDULED: <2023-09-29 Fri>
À faire au bout de 10ans, on attend l’an prochain
**** DONE [#B] Commander pièce
CLOSED: [2023-09-11 Mon 19:18] SCHEDULED: <2023-09-11 Mon>
/Entered on/ [2023-09-11 Mon 19:12]
**** DONE Prendre rendez vous
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
*** DONE Commander pièce courroie de distribution
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
/Entered on/ [2023-09-11 Mon 19:12]
*** DONE Prendre rendez vous courroie distribution
CLOSED: [2023-10-07 Sat 17:48]
*** DONE Changer phare arrière droit
CLOSED: [2023-10-08 Sun 13:24] SCHEDULED: <2023-10-08 Sun>
*** DONE Changer ampoule clignotant arrière droit
CLOSED: [2023-10-19 Thu 17:18] SCHEDULED: <2023-10-19 Thu>
Ampoule commandée

Deletion in projects.org at line 670 [4.123895]

B:BD[56.180] → [56.180:259]

∅:D[56.259] → [57.208:320]

B:BD[57.208] → [57.208:320]

B:BD[57.320] → [28.843:895]

∅:D[58.100] → [48.92:128]

∅:D[51.100] → [48.92:128]

∅:D[59.185] → [48.92:128]

∅:D[60.206] → [48.92:128]

∅:D[61.238] → [48.92:128]

∅:D[28.895] → [48.92:128]

∅:D[15.1073] → [48.92:128]

∅:D[36.1211] → [48.92:128]

B:BD[48.92] → [48.92:128]

B:BD[48.128] → [28.896:942]

∅:D[28.942] → [24.1009:1122]

B:BD[24.1009] → [24.1009:1122]

∅:D[24.1122] → [62.377:468]

B:BD[48.237] → [62.377:468]

∅:D[62.468] → [48.297:537]

B:BD[48.297] → [48.297:537]

B:BD[48.537] → [56.260:279]

B:BD[56.279] → [63.102:183]

∅:D[63.183] → [64.425:461]

∅:D[39.328] → [64.425:461]

∅:D[18.458] → [64.425:461]

∅:D[13.747] → [64.425:461]

∅:D[20.929] → [64.425:461]

∅:D[29.1982] → [64.425:461]

B:BD[64.425] → [64.425:461]

B:BD[64.461] → [63.184:262]

∅:D[63.262] → [18.459:533]

B:BD[64.461] → [18.459:533]

B:BD[18.533] → [5.1368:1449]

∅:D[5.1449] → [63.291:438]

B:BD[63.291] → [63.291:438]

∅:D[63.438] → [39.329:426]

B:BD[29.2093] → [39.329:426]

∅:D[39.426] → [14.4900:5006]

∅:D[17.2041] → [14.4900:5006]

B:BD[14.4900] → [14.4900:5006]

∅:D[65.481] → [64.687:723]

∅:D[14.5006] → [64.687:723]

B:BD[64.687] → [64.687:723]

B:BD[64.723] → [14.5007:5074]

B:BD[14.5074] → [22.427:537]

B:BD[22.537] → [27.444:539]

∅:D[27.539] → [63.503:539]

B:BD[63.503] → [63.503:539]

B:BD[63.539] → [2.15:121]

∅:D[2.121] → [6.555:586]

B:BD[6.555] → [6.555:586]

∅:D[6.586] → [5.1511:1547]

B:BD[5.1511] → [5.1511:1547]

B:BD[5.1547] → [2.122:214]

∅:D[2.214] → [66.365:401]

B:BD[66.365] → [66.365:401]

** DONE Saisie administrative taxe d'habitation
CLOSED: [2023-07-30 Sun 15:02]
/Entered on/ [2023-07-02 Sun 18:20]
Découverte <2023-07-02 Sun>. Virement 100.50€ fait.
Mail envoyé ce jour
** KILL Vendre vélo
CLOSED: [2023-11-02 Thu 22:31]
/Entered on/ [2023-07-29 Sat 10:23]
** DONE Vendre
CLOSED: [2023-11-02 Thu 22:31]
*** DONE Envoyer Dimensions frigo et machine à laver
CLOSED: [2023-10-17 Tue 23:20] SCHEDULED: <2023-10-17 Wed>
** DONE Photo à Éric pour lit
CLOSED: [2023-07-30 Sun 19:07] SCHEDULED: <2023-07-30 Sun>
** DONE SMS annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
/Entered on/ [2023-07-29 Sat 10:25]
** DONE Lettre recommandée annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
#+category: maison
** DONE Résilier box
CLOSED: [2023-10-26 Thu 09:21] SCHEDULED: <2023-10-26 Thu>
/Entered on/ [2023-10-03 Tue 23:11]
Envoyé le mail + règlement intérieur. Ce n'est pas une vrai attestation...
Soit raison impérative (pas de frais), soit logement avec déménagement
** DONE Résilier eau
CLOSED: [2023-11-05 Sun 14:51] SCHEDULED: <2023-11-03 Fri>
À faire après avoir quitté le logement (rétroactif)
** DONE Résilier électricité
CLOSED: [2023-10-26 Thu 09:26] SCHEDULED: <2023-10-26 Thu>
** DONE Résilier ordures ménagères
CLOSED: [2023-10-21 Sat 14:31] SCHEDULED: <2023-10-20 Fri>
Mail envoyé
** DONE Payer ordures ménagères
CLOSED: [2023-10-07 Sat 17:48] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-03 Tue 23:12]
Envoyé TIP. RIB déjà envoyé ? Sinon à repaer <2023-10-07 Sat>
** DONE Course
CLOSED: [2023-10-09 Mon 22:30] SCHEDULED: <2023-10-09 Mon>
/Entered on/ [2023-10-09 Mon 22:09]
** DONE Renvoyer clavier corsair SK
CLOSED: [2023-10-27 Fri 21:14] SCHEDULED: <2023-10-26 Thu>
/Entered on/ [2023-10-26 Thu 09:27]
** DONE Payer facture eau Gennes: à vérifier
CLOSED: [2023-11-10 Fri 16:52] SCHEDULED: <2023-11-09 Thu>
Payé 2023-11-08, à vérifier
/Entered on/ [2023-11-05 Sun 15:28]
** DONE Déposer chèque caution
CLOSED: [2023-11-10 Fri 16:50] SCHEDULED: <2023-11-07 Tue>
/Entered on/ [2023-11-06 Mon 21:00]

Deletion in projects.org at line 674 [4.123895]
B:BD[50.118] → [13.748:859]
∅:D[67.120] → [50.204:240]
∅:D[13.859] → [50.204:240]
∅:D[17.2070] → [50.204:240]
∅:D[29.2122] → [50.204:240]
∅:D[14.5103] → [50.204:240]
B:BD[50.204] → [50.204:240]
B:BD[50.240] → [14.5104:5118]
B:BD[14.5118] → [13.860:916]
```
** DONE Demande remboursement frais compte bancaire
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-25 Wed>
/Entered on/ [2023-08-13 Sun 11:16]
À surveiller
Relancé 2023-10-15 Sun: relance la directrice d'agence
```
Deletion in projects.org at line 687 [4.123895]
B:BD[68.2413] → [56.505:564]
∅:D[56.564] → [69.254:313]
B:BD[69.254] → [69.254:313]
∅:D[69.313] → [70.441:478]
B:BD[70.441] → [70.441:478]
```
*** KILL Gentoo package diagrams-graphviz :gentoo:haskell:
CLOSED: [2023-06-24 Sat 15:43] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:28]
```

Replacement in projects/bisonex.org at line 2 [72.35]

B:BD[71.5112] → [3.658:8850]

ub.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** WAIT [[https://github.com/NixOS/nixpkgs/pull/249329][Multiqc]]
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
** KILL Mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
Packaging faisable mais nombreux paquet python
** TODO Variant validator -> hgvs
C'est juste une interface autour d'hgvs mais il faut
- postgresql
- un accès ou télécharger des bases de données
  Dépendences
  s: wcwidth, pyee, pure-eval, ptyprocess, pickleshare, parsley, parse, fake-useragent, executing, backcall, appdirs, zipp, websockets, w3lib, urllib3, traitlets, tqdm, tabulate, sqlparse, soupsieve, six, pygments, psycopg2, prompt-toolkit, pexpect, parso, lxml, idna, humanfriendly, decorator, cython, cssselect, configparser, charset-normalizer, certifi, attrs, requests, pysam, pyquery, matplotlib-inline, jedi, importlib-metadata, coloredlogs, beautifulsoup4, asttokens, yoyo-migrations, stack-data, pyppeteer, bs4, bioutils, requests-html, ipython, biocommons.seqrepo, hgvs
** TODO SPIP :spip:
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann :T2T:
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** KILL Mise à jour T2T :T2T:
*** WAIT Corriger PR
SCHEDULED: <2023-11-19 Sun>
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
**** WAIT Corriger PR biobigfile
SCHEDULED: <2023-11-19 Sun>
/Entered on/ [2023-10-15 Sun 17:21]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAIT Package Spip https://github.com/NixOS/nixpkgs/pull/247476
** TODO Happy :happy:
*** TODO PR python 3 upstream
SCHEDULED: <2023-11-15 Wed>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-15 Wed>
** PROJ SpliceAI
** TODO Bamsurgeon
/Entered on/ [2023-05-13 Sat 19:11]
*** TODO Velvet
** TODO PR Picard avec option pour gérer la mémoire
Similaire à
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
* Julia :julia:
** KILL XAM.jl: PR pour modification record :julia:
CLOSED: [2023-05-29 Mon 15:40] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:39]
** TODO XAMscissors.jl :xamscissors:
Modification de la séquence dans BAM.
*Pas de mise à jour de CIGAR*
On convertit en fastq et on lance le pipeline pour "corriger"
#+begin_src sh
cd /home/alex/code/bisonex/out/63003856/preprocessing/mapped
samtools view 63003856_S135.bam NC_000022.11 -o 63003856_S135_chr22.bam
cd /home/alex/recherche/bisonex/code/BamScissors.jl
cp ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135_chr22.bam .
samtools index 63003856_chr22.bam
#+end_src
Le script va modifier le bam, le trier et générer le fastq. !!!
Attention: ne pas oublier l'option -n !!!
#+begin_src sh
time julia --project=.. insertVariant.jl
scp 63003856_S135_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
*** WAIT Implémenter les SNV avec VAF :snv:
Stratégie :
1. calculer la profondeur sur les positions
2. créer un dictionnaire { nom du reads : position dataframe }
3. itérer sur tous les reads et changer ceux marqués
**** DONE VAF = 1
CLOSED: [2023-05-29 Mon 15:34]
**** DONE VAF selon loi normale
CLOSED: [2023-05-29 Mon 15:35]
Tronquée si > 1
**** WAIT Tests unitaires
***** DONE NA12878: 1 gène sur chromosome 22
CLOSED: [2023-05-30 Tue 23:55]
root = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/"
#+begin_src sh
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878.bwa.markDuplicates.bam  chr22 -o project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam chr22:19419700-19424000 -o NIST7035_H7AP8ADXX_NA12878_chr22_MRPL40_hg19.bam
#+end_src
***** WAIT Pull request formatspeciment
https://github.com/BioJulia/FormatSpecimens.jl/pull/8
***** DONE Formatspecimens
CLOSED: [2023-05-29 Mon 23:03]
****** DONE 1 read
CLOSED: [2023-05-29 Mon 23:02]
****** DONE VAF sur 1 exon
CLOSED: [2023-05-29 Mon 23:03]
**** DONE [#A] Bug: perte de nombreux reads avec NA12878
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-18 Fri>
:PROPERTIES:
:ID:       5c1c36f3-f68e-4e6d-a7b6-61dca89abc37
:END:
Ex: chrX:g.124056226 : on passe de 65 reads à 1
Test xamscissors: pas de soucis...
On teste sur cette position +/- 200bp
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
samtools view   /home/alex/code/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam chrX:124056026-124056426 -o chrXsmall.bam
#+end_src
#+RESULTS:
***** DONE Vérifier profondeur avec dernière version :
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
****** DONE chr20: profondeur ok
SCHEDULED: <2023-08-19 Sat>
****** DONE toutes les données
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
Ok pour 7 variants (IGV) notament chromosome X
*** TODO Implémenter les indel avec VAF :indel:
*** TODO Soumission paquet
* Données
:PROPERTIES:
:CATEGORY: data
:END:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande

[71.5112]

[73.30]

ub.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** WAIT [[https://github.com/NixOS/nixpkgs/pull/249329][Multiqc]]
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
** KILL Mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
Packaging faisable mais nombreux paquet python
** TODO Variant validator -> hgvs
C'est juste une interface autour d'hgvs mais il faut
- postgresql
- un accès ou télécharger des bases de données
  Dépendences
  s: wcwidth, pyee, pure-eval, ptyprocess, pickleshare, parsley, parse, fake-useragent, executing, backcall, appdirs, zipp, websockets, w3lib, urllib3, traitlets, tqdm, tabulate, sqlparse, soupsieve, six, pygments, psycopg2, prompt-toolkit, pexpect, parso, lxml, idna, humanfriendly, decorator, cython, cssselect, configparser, charset-normalizer, certifi, attrs, requests, pysam, pyquery, matplotlib-inline, jedi, importlib-metadata, coloredlogs, beautifulsoup4, asttokens, yoyo-migrations, stack-data, pyppeteer, bs4, bioutils, requests-html, ipython, biocommons.seqrepo, hgvs
** TODO SPIP :spip:
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann :T2T:
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** KILL Mise à jour T2T :T2T:
*** WAIT Corriger PR
SCHEDULED: <2023-11-19 Sun>
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
**** TODO Corriger PR biobigfile
SCHEDULED: <2023-11-18 Sat>
/Entered on/ [2023-10-15 Sun 17:21]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAIT Package Spip https://github.com/NixOS/nixpkgs/pull/247476
** TODO Happy :happy:
*** TODO PR python 3 upstream
SCHEDULED: <2023-11-15 Wed>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-15 Wed>
** PROJ SpliceAI
** TODO Bamsurgeon
/Entered on/ [2023-05-13 Sat 19:11]
*** TODO Velvet
** TODO PR Picard avec option pour gérer la mémoire
Similaire à
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
* Julia :julia:
** KILL XAM.jl: PR pour modification record :julia:
CLOSED: [2023-05-29 Mon 15:40] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:39]
** TODO XAMscissors.jl :xamscissors:
Modification de la séquence dans BAM.
*Pas de mise à jour de CIGAR*
On convertit en fastq et on lance le pipeline pour "corriger"
#+begin_src sh
cd /home/alex/code/bisonex/out/63003856/preprocessing/mapped
samtools view 63003856_S135.bam NC_000022.11 -o 63003856_S135_chr22.bam
cd /home/alex/recherche/bisonex/code/BamScissors.jl
cp ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135_chr22.bam .
samtools index 63003856_chr22.bam
#+end_src
Le script va modifier le bam, le trier et générer le fastq. !!!
Attention: ne pas oublier l'option -n !!!
#+begin_src sh
time julia --project=.. insertVariant.jl
scp 63003856_S135_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
*** WAIT Implémenter les SNV avec VAF :snv:
Stratégie :
1. calculer la profondeur sur les positions
2. créer un dictionnaire { nom du reads : position dataframe }
3. itérer sur tous les reads et changer ceux marqués
**** DONE VAF = 1
CLOSED: [2023-05-29 Mon 15:34]
**** DONE VAF selon loi normale
CLOSED: [2023-05-29 Mon 15:35]
Tronquée si > 1
**** WAIT Tests unitaires
***** DONE NA12878: 1 gène sur chromosome 22
CLOSED: [2023-05-30 Tue 23:55]
root = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/"
#+begin_src sh
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878.bwa.markDuplicates.bam  chr22 -o project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam chr22:19419700-19424000 -o NIST7035_H7AP8ADXX_NA12878_chr22_MRPL40_hg19.bam
#+end_src
***** WAIT Pull request formatspeciment
https://github.com/BioJulia/FormatSpecimens.jl/pull/8
***** DONE Formatspecimens
CLOSED: [2023-05-29 Mon 23:03]
****** DONE 1 read
CLOSED: [2023-05-29 Mon 23:02]
****** DONE VAF sur 1 exon
CLOSED: [2023-05-29 Mon 23:03]
**** DONE [#A] Bug: perte de nombreux reads avec NA12878
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-18 Fri>
:PROPERTIES:
:ID:       5c1c36f3-f68e-4e6d-a7b6-61dca89abc37
:END:
Ex: chrX:g.124056226 : on passe de 65 reads à 1
Test xamscissors: pas de soucis...
On teste sur cette position +/- 200bp
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
samtools view   /home/alex/code/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam chrX:124056026-124056426 -o chrXsmall.bam
#+end_src
#+RESULTS:
***** DONE Vérifier profondeur avec dernière version :
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
****** DONE chr20: profondeur ok
SCHEDULED: <2023-08-19 Sat>
****** DONE toutes les données
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
Ok pour 7 variants (IGV) notament chromosome X
*** TODO Implémenter les indel avec VAF :indel:
*** TODO Soumission paquet
* Données
:PROPERTIES:
:CATEGORY: data
:END:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande

Replacement in projects/bisonex.org at line 30 [72.35]

B:BD[74.49126] → [74.49126:49127]

B:BD[74.49127] → [66.8610:16801]


*** DONE Biblio performance aligneur <(biblio aligneur)> <(aligneur)>
CLOSED: [2023-10-13 Fri 17:40] SCHEDULED: <2023-10-01 Sun>
*** DONE Figure: nombre d'articles citant les principaux aligneur par année
CLOSED: [2023-10-11 Wed 23:54] SCHEDULED: <2023-10-03 Tue>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
*** DONE Figure: nombre d'articles citant les principaux aligneur
CLOSED: [2023-10-12 Thu 23:58] SCHEDULED: <2023-10-12 Thu>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
On se base sur
** Appel de variant
*** TODO Biblio <(biblio appel variant)> <(appel variant)>
SCHEDULED: <2023-11-07 Tue>
*** TODO Figure: nombre de publication par appel de variant
SCHEDULED: <2023-11-07 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-11-16 Thu>
/Entered on/ [2023-09-19 Tue 08:43]
* Tests :tests:
** KILL Non régression : version prod
CLOSED: [2023-05-23 Tue 08:46]
*** DONE ID common snp
CLOSED: [2022-11-19 Sat 21:36]
#+begin_src
$ wc -l ID_of_common_snp.txt
23194290 ID_of_common_snp.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
23194290 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
#+end_src
*** DONE ID common snp not clinvar patho
CLOSED: [2022-12-11 Sun 20:11]
**** DONE Vérification du problème
CLOSED: [2022-12-11 Sun 16:30]
Sur le J:
21155134 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref
Version de "non-régression"
21155076 database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
Nouvelle version
23193391 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
Si on enlève les doublons
$ sort database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > old.txt
$ wc -l old.txt
21107097 old.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > new.txt
$ wc -l new.txt
21174578 new.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref | uniq > ref.txt
$ wc -l ref.txt
21107155 ref.txt
Si on regarde la différence
 comm -23 ref.txt old.txt
rs1052692
rs1057518973
rs1057518973
rs11074121
rs112848754
rs12573787
rs145033890
rs147889095
rs1553904159
rs1560294695
rs1560296615
rs1560310926
rs1560325547
rs1560342418
rs1560356225
rs1578287542
...
On cherche le premier
bcftools query -i 'ID="rs1052692"' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 1619351 C A,T
Il est bien patho...
$ bcftools query -i 'POS=1619351' database/clinvar/clinvar.vcf.gz -f '%CHROM %POS %REF %ALT %INFO/CLNSIG\n'
19 1619351 C T Conflicting_interpretations_of_pathogenicity
On vérifie pour tous les autres
$ comm -23 ref.txt old.txt > tocheck.txt
On génère les régions à vérifier (chromosome number:position)
$ bcftools query -i 'ID=@tocheck.txt' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM\t%POS\n' > tocheck.pos
On génère le mapping inverse (chromosome number -> NC)
$ awk ' { t = $1; $1 = $2; $2 = t; print; } ' database/RefSeq/refseq_to_number_only_consensual.txt  > mapping.txt
On remap clinvar
$ bcftools annotate --rename-chrs mapping.txt database/clinvar/clinvar.vcf.gz -o clinvar_remapped.vcf.gz
$ tabix clinvar_remapped.vcf.gz
Enfin, on cherche dans clinvar la classification
$ bcftools query -R tocheck.pos clinvar_remapped.vcf.gz -f '%CHROM %POS %INFO/CLNSIG\n'
$ bcftools query -R tocheck.pos database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %ID \n' | grep '^NC'
#+RESULTS:
**** DONE Comprendre pourquoi la nouvelle version donne un résultat différent
CLOSED: [2022-12-11 Sun 20:11]
***** DONE Même version dbsnp et clinvar ?
CLOSED: [2022-12-10 Sat 23:02]
Clinvar différent !
  $ bcftools stats clinvar.gz
  clinvar (Alexis)
SN	0	number of samples:	0
SN	0	number of records:	1492828
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338007
SN	0	number of MNPs:	5562
SN	0	number of indels:	144580
SN	0	number of others:	3714
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
clinvar (new)
SN	0	number of samples:	0
SN	0	number of records:	1493470
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338561
SN	0	number of MNPs:	5565
SN	0	number of indels:	144663
SN	0	number of others:	3716
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
***** DONE Mettre à jour clinvar et dbnSNP pour travailler sur les mêm bases
CLOSED: [2022-12-11 Sun 12:10]
Problème persiste
***** DONE Supprimer la conversion en int du chromosome
CLOSED: [2022-12-10 Sat 19:29]
***** KILL Même NC ?
CLOSED: [2022-12-10 Sat 19:29]
$  zgrep "contig=<ID=NC_\(.*\)" clinvar/GRCh38/clinvar.vcf.gz > contig.clinvar
$ diff contig.txt contig.clinvar
< ##contig=<ID=NC_012920.1>
***** DONE Tester sur chromosome 19: ok
CLOSED: [2022-12-11 Sun 13:53]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clinvar_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_old.vcf.gz
 bcftools filter -i 'CHROM="19"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_old.vcf.gz
#+end_src
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535194 | new.txt |
| 1070349 | total   |
Si on prend le premier manquant dans new, il est conflicting patho donc il ne devrait pas y être...
$ bcftools query -i 'ID="rs10418277"' dbSNP
_common_19.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'ID="rs10418277"' dbSNP_common_19_old.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'POS=54939682' clinvar_19.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ bcftools query -i 'POS=54939682' clinvar_19_old.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ grep rs10418277 *.txt
new.txt:rs10418277
tmp.txt:rs10418277
Le problème venait de la POS qui n'était plus convertie en int (suppression de la ligne par erreur ??)
On vérifie
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
diff old.txt new.txt
#+end

[74.49126]

[66.16801]


*** DONE Biblio performance aligneur <(biblio aligneur)> <(aligneur)>
CLOSED: [2023-10-13 Fri 17:40] SCHEDULED: <2023-10-01 Sun>
*** DONE Figure: nombre d'articles citant les principaux aligneur par année
CLOSED: [2023-10-11 Wed 23:54] SCHEDULED: <2023-10-03 Tue>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
*** DONE Figure: nombre d'articles citant les principaux aligneur
CLOSED: [2023-10-12 Thu 23:58] SCHEDULED: <2023-10-12 Thu>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
On se base sur
** Appel de variant
*** TODO Biblio <(biblio appel variant)> <(appel variant)>
SCHEDULED: <2023-11-07 Tue>
*** TODO Figure: nombre de publication par appel de variant
SCHEDULED: <2023-11-07 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-11-19 Sun>
/Entered on/ [2023-09-19 Tue 08:43]
* Tests :tests:
** KILL Non régression : version prod
CLOSED: [2023-05-23 Tue 08:46]
*** DONE ID common snp
CLOSED: [2022-11-19 Sat 21:36]
#+begin_src
$ wc -l ID_of_common_snp.txt
23194290 ID_of_common_snp.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
23194290 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
#+end_src
*** DONE ID common snp not clinvar patho
CLOSED: [2022-12-11 Sun 20:11]
**** DONE Vérification du problème
CLOSED: [2022-12-11 Sun 16:30]
Sur le J:
21155134 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref
Version de "non-régression"
21155076 database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
Nouvelle version
23193391 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
Si on enlève les doublons
$ sort database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > old.txt
$ wc -l old.txt
21107097 old.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > new.txt
$ wc -l new.txt
21174578 new.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref | uniq > ref.txt
$ wc -l ref.txt
21107155 ref.txt
Si on regarde la différence
 comm -23 ref.txt old.txt
rs1052692
rs1057518973
rs1057518973
rs11074121
rs112848754
rs12573787
rs145033890
rs147889095
rs1553904159
rs1560294695
rs1560296615
rs1560310926
rs1560325547
rs1560342418
rs1560356225
rs1578287542
...
On cherche le premier
bcftools query -i 'ID="rs1052692"' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 1619351 C A,T
Il est bien patho...
$ bcftools query -i 'POS=1619351' database/clinvar/clinvar.vcf.gz -f '%CHROM %POS %REF %ALT %INFO/CLNSIG\n'
19 1619351 C T Conflicting_interpretations_of_pathogenicity
On vérifie pour tous les autres
$ comm -23 ref.txt old.txt > tocheck.txt
On génère les régions à vérifier (chromosome number:position)
$ bcftools query -i 'ID=@tocheck.txt' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM\t%POS\n' > tocheck.pos
On génère le mapping inverse (chromosome number -> NC)
$ awk ' { t = $1; $1 = $2; $2 = t; print; } ' database/RefSeq/refseq_to_number_only_consensual.txt  > mapping.txt
On remap clinvar
$ bcftools annotate --rename-chrs mapping.txt database/clinvar/clinvar.vcf.gz -o clinvar_remapped.vcf.gz
$ tabix clinvar_remapped.vcf.gz
Enfin, on cherche dans clinvar la classification
$ bcftools query -R tocheck.pos clinvar_remapped.vcf.gz -f '%CHROM %POS %INFO/CLNSIG\n'
$ bcftools query -R tocheck.pos database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %ID \n' | grep '^NC'
#+RESULTS:
**** DONE Comprendre pourquoi la nouvelle version donne un résultat différent
CLOSED: [2022-12-11 Sun 20:11]
***** DONE Même version dbsnp et clinvar ?
CLOSED: [2022-12-10 Sat 23:02]
Clinvar différent !
  $ bcftools stats clinvar.gz
  clinvar (Alexis)
SN	0	number of samples:	0
SN	0	number of records:	1492828
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338007
SN	0	number of MNPs:	5562
SN	0	number of indels:	144580
SN	0	number of others:	3714
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
clinvar (new)
SN	0	number of samples:	0
SN	0	number of records:	1493470
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338561
SN	0	number of MNPs:	5565
SN	0	number of indels:	144663
SN	0	number of others:	3716
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
***** DONE Mettre à jour clinvar et dbnSNP pour travailler sur les mêm bases
CLOSED: [2022-12-11 Sun 12:10]
Problème persiste
***** DONE Supprimer la conversion en int du chromosome
CLOSED: [2022-12-10 Sat 19:29]
***** KILL Même NC ?
CLOSED: [2022-12-10 Sat 19:29]
$  zgrep "contig=<ID=NC_\(.*\)" clinvar/GRCh38/clinvar.vcf.gz > contig.clinvar
$ diff contig.txt contig.clinvar
< ##contig=<ID=NC_012920.1>
***** DONE Tester sur chromosome 19: ok
CLOSED: [2022-12-11 Sun 13:53]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clinvar_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_old.vcf.gz
 bcftools filter -i 'CHROM="19"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_old.vcf.gz
#+end_src
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535194 | new.txt |
| 1070349 | total   |
Si on prend le premier manquant dans new, il est conflicting patho donc il ne devrait pas y être...
$ bcftools query -i 'ID="rs10418277"' dbSNP
_common_19.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'ID="rs10418277"' dbSNP_common_19_old.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'POS=54939682' clinvar_19.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ bcftools query -i 'POS=54939682' clinvar_19_old.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ grep rs10418277 *.txt
new.txt:rs10418277
tmp.txt:rs10418277
Le problème venait de la POS qui n'était plus convertie en int (suppression de la ligne par erreur ??)
On vérifie
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
diff old.txt new.txt
#+end

Replacement in projects/bisonex.org at line 63 [72.35]

B:BD[14.49719] → [32.314:8506]

    0.529245 |
Hg38
| Type  | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision |
| INDEL |         549 |      489 |       60 |         899 |       64 |       340 |     8 |    17 |      0.890710 |         0.885510 |
| SNP   |       21973 |    21462 |      511 |       26285 |      563 |      4263 |    68 |    16 |      0.976744 |         0.974435 |
****** DONE Interesection des bed: similaire
CLOSED: [2023-07-04 Tue 23:11]
HG38
 #+begin_src sh
 bedtools intersect -a capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed -b /Work/Groups/bisonex/data/giab/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed  | wc -l
 #+end_src
 204280
 T2T
 #+begin_src sh
 bedtools intersect -a /Work/Groups/bisonex/data/giab/T2T/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed -b /Work/Groups/bisonex/data/giab/T2T/HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed  | wc -l
 #+end_src
 204021
****** DONE Vérifier la ligne de commande
CLOSED: [2023-07-04 Tue 23:38]
#+begin_src sh
hap.py \
    HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz \
    HG001-SRX11061486_SRR14724513-T2T.vcf.gz \
     \
    --reference chm13v2.0.fa \
    --threads 6 \
     \
    -T Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed \
    --false-positives HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed \
     \
    -o HG001
#+end_src
****** DONE Corriger FILTER : mieux mais toujours trop de négatifs. 3/4 SNP retrouvés
CLOSED: [2023-07-08 Sat 15:19] SCHEDULED: <2023-07-08 Sat>
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL          413       246       167          751       289        215      2     98       0.595642          0.460821        0.286285         0.519629                     NaN                     NaN                   2.428571                   2.465116
INDEL   PASS          413       246       167          751       289        215      2     98       0.595642          0.460821        0.286285         0.519629                     NaN                     NaN                   2.428571                   2.465116
  SNP    ALL        15883     15479       404        23597      5277       2841     46     44       0.974564          0.745760        0.120397         0.844947                3.017198                 2.85705                   5.560099                   2.114633
  SNP   PASS        15883     15479       404        23597      5277       2841     46     44       0.974564          0.745760        0.120397         0.844947                3.017198                 2.85705                   5.560099                   2.114633
******* DONE Vérifier qu'il ne reste plus de filtre autre que PASS
CLOSED: [2023-07-08 Sat 15:19]
#+begin_src
$ zgrep -c 'PASS' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730505
$ zgrep -c '^chr' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730506
#+end_src
****** TODO 1/4 SNP manquant ?
******* DONE Regarder avec Julia si ce sont vraiment des FP: 61/5277 qui ne le sont pas
CLOSED: [2023-07-09 Sun 12:09]
******* DONE Examiner les FP
CLOSED: [2023-07-30 Sun 22:05]
******* DONE Tester un FP
CLOSED: [2023-07-30 Sun 22:05]
  2 │ chr1        608765  A           G           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:ti:SNP:homalt:188
  liftDown UCSC: rien en GIAB : vrai FP
 3 │ chr1        762943  A           G           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:ti:SNP:homalt:287
 4 │ chr1        762945  A           T           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:tv:SNP:homalt:287
 Remaniements complexes ? Pas dans le gène en HG38
******* DONE La plupart des FP (4705/5566) sont homozygotes: erreur de référence ?
CLOSED: [2023-07-12 Wed 21:10] SCHEDULED: <2023-07-09 Sun>
Sur les 2 premiers variants, ils montrent en fait la différence entre T2T et GRCh38
Erreur à l'alignement ?
******** KILL relancer l'alignement
CLOSED: [2023-07-09 Sun 17:36]
******** DONE vérifier reads identiques hg38 et T2T: oui
CLOSED: [2023-07-09 Sun 16:36]
T2T CHR1608765
38   	chr1:1180168-1180168 (
SRR14724513.24448214
SRR14724513.24448214
******* DONE Vérifier quelques variants sur IGV
CLOSED: [2023-07-09 Sun 17:36]
******* KILL Répartition des FP : cluster ?
CLOSED: [2023-07-09 Sun 17:36]
****** DONE Examiner les FP restant après correction selon séquence de référence
CLOSED: [2023-08-12 Sat 15:57]
****** HOLD Examiner les variants supprimé
****** TODO Enlever les FP qui correspondent à un changement dans le génome
******* Condition:
- pas de variation à la position en GRCh38
- variantion homozygote
- la varation en T2T correspond au changement de pair de base GRC38 -> T2T
  pour les SNP:
  alt_T2T[i] = DNA_GRC38[j]
  avec i la position en T2T et j la position en GRCh38
  Note: définir un ID n'est pas correct car les variants peuvent être modifié par happy !
******* Idée
 - Pour chaque FP, c'est un "faux" FP si
     - REF en hg38 == ALT en T2T
     - et REF en hg38 != REF en T2T
     - et variant homozygote
Comment obtenir les séquences de réferences ?
1. liftover
2. blat sur la séquence autour du variant
3. identifier quelques reads contenant le variant et regarder leur aligneement en hg38
Après discussion avec Alexis: solution 3
******* Algorithme
1. Extraire les coordonnées en T2T des faux positifs *homozygote*
2. Pour chaque faux positif
   1. lister 10 reads contenant le variant
   2. pour chacun de ces reads, récupérer la séquence en T2T et GRCh38 via le nom du read dans le bam
   3. si la séquence en T2T modifiée par le variant est "identique" à celle en GRCh38, alors on ignore ce faux positif
Note: on ignore les reads qui ont changé de chromosome entre les version
******* DONE Résultat préliminaire
CLOSED: [2023-07-23 Sun 14:30]
cf [[file:~/roam/research/bisonex/code/giab/giab-corrected.csv][script julia]]
3498 faux positifs en moins, soit 0.89 sensibilité
julia> tp=15479
julia> fp=5277
julia> tp/(tp+fp)
0.7457602620928888
julia> tp/(tp+(fp-3498))
0.8969173716537258
On est toujours en dessous des 97%
******* HOLD Corriger proprement VCF ou résultats Happy
******* TODO Adapter pour gérer plusieurs variants par read
****** DONE Méthodologie du pangenome
CLOSED: [2023-10-03 Tue 21:28]
Voir biblio[cite:@liao2023]  mais ont aligné sur GRCH38
******* DONE Mail alexis
CLOSED: [2023-10-03 Tue 21:28]
****** DONE Méthodologie T2T
CLOSED: [2023-10-16 Mon 19:42]
Mail alexis
SCHEDULED: <2023-10-04 Wed>
***** TODO Rendre simplement le nombre de vrais positifs
SCHEDULED: <2023-11-17 Fri>
***** KILL Mail Yannis
CLOSED: [2023-07-08 Sat 10:44]
***** DONE Mail GIAB pour version T2T
CLOSED: [2023-07-07 Fri 18:37]
**** TODO HG002 :hg002:T2T:
**** TODO HG003 :hg003:T2T:
**** TODO HG004 :hg004:T2T:
**** DONE Plot : ashkenazim trio :hg38:
CLOSED: [2023-07-30 Sun 16:49] SCHEDULED: <2023-07-30 Sun 15:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 16:06]--[2023-07-30 Sun 16:35] =>  0:29
CLOCK: [2023-07-30 Sun 15:39]--[2023-07-30 Sun 15:40] =>  0:01
:END:
/Entered on/ [2023-04-16 Sun 17:29]
Refaire résultats
**** DONE Mail Paul sur les résultat ashkenazim +/- centogene
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Relancer comparaison GIAB avec GATK 4.4.0
CLOSED: [2023-08-12 Sat 15:55]
/Entered on/ [2023-08-03 Thu 12:42]
*** TODO Platinum genome :platinum:
https://emea.illumina.com/platinumgenomes.html
**** TODO Tester sur la zone couverte par l'exome centogène
SCHEDULED: <2023-11-17 Fri>
*** DONE Séquencer NA12878 :cento:hg001:
CLOSED: [2023-10-07 Sat 17:59]
Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN
**** DONE ADN commandé
CLOSED: [2023-06-30 Fri 22:29]
**** DONE Sauvegarder les données brutes
CLOSED: [2023-07-30 Sun 14:22] SCHEDULED: <2023-07-19 Wed>
K, scality, S
**** KILL Récupérer le fichier de capture
CLOSED: [20

[14.49719]

[3.8851]

    0.529245 |
Hg38
| Type  | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision |
| INDEL |         549 |      489 |       60 |         899 |       64 |       340 |     8 |    17 |      0.890710 |         0.885510 |
| SNP   |       21973 |    21462 |      511 |       26285 |      563 |      4263 |    68 |    16 |      0.976744 |         0.974435 |
****** DONE Interesection des bed: similaire
CLOSED: [2023-07-04 Tue 23:11]
HG38
 #+begin_src sh
 bedtools intersect -a capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed -b /Work/Groups/bisonex/data/giab/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed  | wc -l
 #+end_src
 204280
 T2T
 #+begin_src sh
 bedtools intersect -a /Work/Groups/bisonex/data/giab/T2T/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed -b /Work/Groups/bisonex/data/giab/T2T/HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed  | wc -l
 #+end_src
 204021
****** DONE Vérifier la ligne de commande
CLOSED: [2023-07-04 Tue 23:38]
#+begin_src sh
hap.py \
    HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz \
    HG001-SRX11061486_SRR14724513-T2T.vcf.gz \
     \
    --reference chm13v2.0.fa \
    --threads 6 \
     \
    -T Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed \
    --false-positives HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed \
     \
    -o HG001
#+end_src
****** DONE Corriger FILTER : mieux mais toujours trop de négatifs. 3/4 SNP retrouvés
CLOSED: [2023-07-08 Sat 15:19] SCHEDULED: <2023-07-08 Sat>
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL          413       246       167          751       289        215      2     98       0.595642          0.460821        0.286285         0.519629                     NaN                     NaN                   2.428571                   2.465116
INDEL   PASS          413       246       167          751       289        215      2     98       0.595642          0.460821        0.286285         0.519629                     NaN                     NaN                   2.428571                   2.465116
  SNP    ALL        15883     15479       404        23597      5277       2841     46     44       0.974564          0.745760        0.120397         0.844947                3.017198                 2.85705                   5.560099                   2.114633
  SNP   PASS        15883     15479       404        23597      5277       2841     46     44       0.974564          0.745760        0.120397         0.844947                3.017198                 2.85705                   5.560099                   2.114633
******* DONE Vérifier qu'il ne reste plus de filtre autre que PASS
CLOSED: [2023-07-08 Sat 15:19]
#+begin_src
$ zgrep -c 'PASS' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730505
$ zgrep -c '^chr' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730506
#+end_src
****** TODO 1/4 SNP manquant ?
******* DONE Regarder avec Julia si ce sont vraiment des FP: 61/5277 qui ne le sont pas
CLOSED: [2023-07-09 Sun 12:09]
******* DONE Examiner les FP
CLOSED: [2023-07-30 Sun 22:05]
******* DONE Tester un FP
CLOSED: [2023-07-30 Sun 22:05]
  2 │ chr1        608765  A           G           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:ti:SNP:homalt:188
  liftDown UCSC: rien en GIAB : vrai FP
 3 │ chr1        762943  A           G           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:ti:SNP:homalt:287
 4 │ chr1        762945  A           T           ./.:.:.:.:NOCALL:nocall:.  1/1:FP:.:tv:SNP:homalt:287
 Remaniements complexes ? Pas dans le gène en HG38
******* DONE La plupart des FP (4705/5566) sont homozygotes: erreur de référence ?
CLOSED: [2023-07-12 Wed 21:10] SCHEDULED: <2023-07-09 Sun>
Sur les 2 premiers variants, ils montrent en fait la différence entre T2T et GRCh38
Erreur à l'alignement ?
******** KILL relancer l'alignement
CLOSED: [2023-07-09 Sun 17:36]
******** DONE vérifier reads identiques hg38 et T2T: oui
CLOSED: [2023-07-09 Sun 16:36]
T2T CHR1608765
38   	chr1:1180168-1180168 (
SRR14724513.24448214
SRR14724513.24448214
******* DONE Vérifier quelques variants sur IGV
CLOSED: [2023-07-09 Sun 17:36]
******* KILL Répartition des FP : cluster ?
CLOSED: [2023-07-09 Sun 17:36]
****** DONE Examiner les FP restant après correction selon séquence de référence
CLOSED: [2023-08-12 Sat 15:57]
****** HOLD Examiner les variants supprimé
****** TODO Enlever les FP qui correspondent à un changement dans le génome
******* Condition:
- pas de variation à la position en GRCh38
- variantion homozygote
- la varation en T2T correspond au changement de pair de base GRC38 -> T2T
  pour les SNP:
  alt_T2T[i] = DNA_GRC38[j]
  avec i la position en T2T et j la position en GRCh38
  Note: définir un ID n'est pas correct car les variants peuvent être modifié par happy !
******* Idée
 - Pour chaque FP, c'est un "faux" FP si
     - REF en hg38 == ALT en T2T
     - et REF en hg38 != REF en T2T
     - et variant homozygote
Comment obtenir les séquences de réferences ?
1. liftover
2. blat sur la séquence autour du variant
3. identifier quelques reads contenant le variant et regarder leur aligneement en hg38
Après discussion avec Alexis: solution 3
******* Algorithme
1. Extraire les coordonnées en T2T des faux positifs *homozygote*
2. Pour chaque faux positif
   1. lister 10 reads contenant le variant
   2. pour chacun de ces reads, récupérer la séquence en T2T et GRCh38 via le nom du read dans le bam
   3. si la séquence en T2T modifiée par le variant est "identique" à celle en GRCh38, alors on ignore ce faux positif
Note: on ignore les reads qui ont changé de chromosome entre les version
******* DONE Résultat préliminaire
CLOSED: [2023-07-23 Sun 14:30]
cf [[file:~/roam/research/bisonex/code/giab/giab-corrected.csv][script julia]]
3498 faux positifs en moins, soit 0.89 sensibilité
julia> tp=15479
julia> fp=5277
julia> tp/(tp+fp)
0.7457602620928888
julia> tp/(tp+(fp-3498))
0.8969173716537258
On est toujours en dessous des 97%
******* HOLD Corriger proprement VCF ou résultats Happy
******* TODO Adapter pour gérer plusieurs variants par read
****** DONE Méthodologie du pangenome
CLOSED: [2023-10-03 Tue 21:28]
Voir biblio[cite:@liao2023]  mais ont aligné sur GRCH38
******* DONE Mail alexis
CLOSED: [2023-10-03 Tue 21:28]
****** DONE Méthodologie T2T
CLOSED: [2023-10-16 Mon 19:42]
Mail alexis
SCHEDULED: <2023-10-04 Wed>
***** TODO Rendre simplement le nombre de vrais positifs
SCHEDULED: <2023-11-22 Wed>
***** KILL Mail Yannis
CLOSED: [2023-07-08 Sat 10:44]
***** DONE Mail GIAB pour version T2T
CLOSED: [2023-07-07 Fri 18:37]
**** TODO HG002 :hg002:T2T:
**** TODO HG003 :hg003:T2T:
**** TODO HG004 :hg004:T2T:
**** DONE Plot : ashkenazim trio :hg38:
CLOSED: [2023-07-30 Sun 16:49] SCHEDULED: <2023-07-30 Sun 15:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 16:06]--[2023-07-30 Sun 16:35] =>  0:29
CLOCK: [2023-07-30 Sun 15:39]--[2023-07-30 Sun 15:40] =>  0:01
:END:
/Entered on/ [2023-04-16 Sun 17:29]
Refaire résultats
**** DONE Mail Paul sur les résultat ashkenazim +/- centogene
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Relancer comparaison GIAB avec GATK 4.4.0
CLOSED: [2023-08-12 Sat 15:55]
/Entered on/ [2023-08-03 Thu 12:42]
*** TODO Platinum genome :platinum:
https://emea.illumina.com/platinumgenomes.html
**** TODO Tester sur la zone couverte par l'exome centogène
SCHEDULED: <2023-11-22 Wed>
*** DONE Séquencer NA12878 :cento:hg001:
CLOSED: [2023-10-07 Sat 17:59]
Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN
**** DONE ADN commandé
CLOSED: [2023-06-30 Fri 22:29]
**** DONE Sauvegarder les données brutes
CLOSED: [2023-07-30 Sun 14:22] SCHEDULED: <2023-07-19 Wed>
K, scality, S
**** KILL Récupérer le fichier de capture
CLOSED: [20

Replacement in projects/bisonex.org at line 79 [72.35]

B:BD[13.43603] → [32.16699:33083]

r preferred)
"Wherever possible we would discourage you from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-11-15 Wed>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
 Row │ variant              meanQual  depth
     │ String               Float64   Int64
─────┼──────────────────────────────────────
   1 │ chr12:g.13594572      60.0      1
   2 │ chr17:g.10204026      60.0      1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep   : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-11-17 Fri>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)>  <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
- [X] 100222_63015289
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- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués :checkpipeline:
SCHEDULED: <2023-10-21 Sat>
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753  noté CG->C
GT:AD:DP:GQ:PL	0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE Un seul exécutable pour toutes les étapes
CLOSED: [2023-11-04 Sat 19:00] SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv  | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv  | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** DONE Parser coordonnée patient
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
**** DONE Un seul type de données
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
***** DONE Vérifier avec derniere version sauvegardé
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
->
patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
- [ ] Fusionner coding,codingPos,codingChange
- [ ] Ne pas écrire proteinchange
- [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic  puis gene, etc
- [ ] Fichier de référence : renommer header
- [ ] vérifier que fichier toujours identique
#+begin_src julia
using DataFramesMeta, CSV
# - [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic  puis gene, etc
# - [ ] Fichier de référence : renommer header
# - [ ] vérifier que fichier toujours identique
#file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
#->
#patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
function mergeCoding(c, p, ch)
    "negatif" in [c, p, ch] ? "negatif" : c * p * ch
end
function negative(t, pos)
    t == "negatif" ? -1 : pos
end
cols = [:patient,:"transcript (cento)",:"transcript (canonical)",:coding,:"genomic (hg38)",
        :"classification (cento)",:zygosity,:gene,:"Confirmed in sanger",:"Found by bisonex",
        :chrom,:pos,:ref,:alt]
d = @chain CSV.read("variant_extracted.csv", DataFrame) begin
    # Fusionner coding,codingPos,codingChange
    @transform :coding = mergeCoding.(:coding, :codingPos, :codingChange)
    # Ne pas écrire proteinchange
    @select $(Not([:codingPos, :codingChange, :proteinChange]))
    # Add missing mcolumns
    @rename :"transcript (cento)" = :transcript :patient = :file :"classification (cento)" = :classification
    @transform :"transcript (canonical)" = missing :"genomic (hg38)" = missing :gene = missing
    @transform :"Confirmed in sanger" = missing :"Found by bisonex" = missing
    @transform :chrom = missing :pos = missing :ref = missing :alt = missing
    # Rorder
    @select :patient :"transcript (cento)" :"transcript (canonical)" :coding :"genomic (hg38)" :"classification (cento)" :zygosity :gene :"Confirmed in sanger" :"Found by bisonex" :chrom :pos :ref :alt
    # Set -1 for negative variant
    @rtransform :pos = :"transcript (cento)" == "negatif" ? -1 : :pos
    @rtransform :"transcript (canonical)"= :"transcript (cento)" == "negatif" ? "negatif" : :"transcript (canonical)"
    @rtransform :"genomic (hg38)" = :"transcript (cento)" == "negatif" ? "negatif" : :"genomic (hg38)"
    @rtransform :coding = :"transcript (cento)" == "negatif" ? "negatif" : :coding
    @rtransform :gene = :"transcript (cento)" == "negatif" ? "negatif" : :gene
    @rtransform :pos = ismissing(:pos) ? -1 : :pos
    end
CSV.write("variant_extracted_remap.csv", d)
d2 = @chain CSV.read("extracted.csv", DataFrame) begin
    @orderby :patient
    end
CSV.write("extracted_sorted.csv", d2)
#+end_src
ON trie les fichiers pour bien avoir le bon order (sinon diff ne fonctionne pas ??)
diff extracted_sorted.csv variant_extracted_remap.csv  -u | save extracted.diff
 patch -p1 extracted_sorted.csv extracted.diff
patching file extracted_sorted.csv
diff extracted_sorted.csv variant_extracted_remap.csv  -u
**** KILL variant_recoder pour avoir les coordonnées VCF
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
mobidetails n   e trouve pas les ieux transcrits
**** DONE Annotation mobidetails (gene + données gonémique)
CLOSED: [2023-10-25 Wed 09:14]
**** DONE Envoyer liste à Paul
SCHEDULED: <2023-10-26 Thu>
**** DONE compare chaque variant avec la sortie du pipeline
CLOSED: [2023-10-31 Tue 00:18] SCHEDULED: <2023-10-21 Sat>
Avec la fonction "test" dans Search.hs
1126 extracted
654 annotated
253 raw data
102 raw and annotated
236 raw and extracted
17 raw NOT extracted
890 extract WITHOUT raw
#+begin_src sh
❯ open diff.txt | from csv | get id | into string | each {|e| "~/annex/data/centogene/reports/" ++ $e ++ "*.pdf"} | each {|e| firefox $e }
#+end_src
Les 17 manquants sont
- 62913191 : CNV
- 62959388 : MT-ATP6
- 62999572 : MT-ATP6
- 62999627 : CNV
- 62999630 : CNV
- 63004218: CNV
- 63006466 : CNV
- 63009152 : manqué à extraire -> bien présent
- 63015289: CNV
- 63024910 : MT-ATP6
- 63040251 : CNV
- 63043050 : CNV
- 63118093 : NA12878
- NA12878 x4
*** DONE Comparer variants cento à sortie bisonex: 50/121 confirmé en sanger, 71/121 non testé, 0 confirmés manqué par pipeline, 5 manqué mais non confirmés
CLOSED: [2023-11-08 Wed 00:19] SCHEDULED: <2023-11-04 Sat>
*** Comparger sanger : variant seul
Compliqué de reconstituer l'arbre familial. L'information est là mais demande du travail.
ON suppose que le variant n'est que dans la famille....
Résultats
❯ open sa

[13.43603]

[75.183]

r preferred)
"Wherever possible we would discourage you from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-11-19 Sun>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
 Row │ variant              meanQual  depth
     │ String               Float64   Int64
─────┼──────────────────────────────────────
   1 │ chr12:g.13594572      60.0      1
   2 │ chr17:g.10204026      60.0      1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep   : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-11-22 Wed>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)>  <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
- [X] 2100422923_62952677
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- [X] 2100601558_62903840
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- [X] 2200146652_62959388
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- [X] 2200694535_63042853
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- [X] 2200699345_63040238
- [X] 2200699383_63043050
- [X] 2200699412_63040731
- [X] 220071551_63048935
- [X] 2200731515_63048963
- [X] 2200748145_63051198
- [X] 2200748171_63051213
- [X] 2200751046_63051249
- [X] 2200751101_63051234
- [X] 2200766471_63054590
- [X] 2200767731_63054595
- [X] 2200767822_63054464
- [X] 2200775505_63060410
- [X] 2200850441_63019345
- [X] 220597589_63026879
- [X] 2300003253_63060430
- [X] 2300005679_63060370
- [X] 2300009914_63060390
- [X] 2300028784_63060001
- [X] 2300036815_63063357
- [X] 2300055382_63061874
- [X] 2300055421_63061871
- [X] 2300055440_63061880
- [X] 230006894_63064950
- [X] 2300071111_63070356
- [X] 2300083434_63071675
- [X] 2300103609_63076239
- [X] 2300104572_63076232
- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués :checkpipeline:
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753  noté CG->C
GT:AD:DP:GQ:PL	0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE Un seul exécutable pour toutes les étapes
CLOSED: [2023-11-04 Sat 19:00] SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv  | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv  | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** DONE Parser coordonnée patient
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
**** DONE Un seul type de données
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
***** DONE Vérifier avec derniere version sauvegardé
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
->
patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
- [ ] Fusionner coding,codingPos,codingChange
- [ ] Ne pas écrire proteinchange
- [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic  puis gene, etc
- [ ] Fichier de référence : renommer header
- [ ] vérifier que fichier toujours identique
#+begin_src julia
using DataFramesMeta, CSV
# - [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic  puis gene, etc
# - [ ] Fichier de référence : renommer header
# - [ ] vérifier que fichier toujours identique
#file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
#->
#patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
function mergeCoding(c, p, ch)
    "negatif" in [c, p, ch] ? "negatif" : c * p * ch
end
function negative(t, pos)
    t == "negatif" ? -1 : pos
end
cols = [:patient,:"transcript (cento)",:"transcript (canonical)",:coding,:"genomic (hg38)",
        :"classification (cento)",:zygosity,:gene,:"Confirmed in sanger",:"Found by bisonex",
        :chrom,:pos,:ref,:alt]
d = @chain CSV.read("variant_extracted.csv", DataFrame) begin
    # Fusionner coding,codingPos,codingChange
    @transform :coding = mergeCoding.(:coding, :codingPos, :codingChange)
    # Ne pas écrire proteinchange
    @select $(Not([:codingPos, :codingChange, :proteinChange]))
    # Add missing mcolumns
    @rename :"transcript (cento)" = :transcript :patient = :file :"classification (cento)" = :classification
    @transform :"transcript (canonical)" = missing :"genomic (hg38)" = missing :gene = missing
    @transform :"Confirmed in sanger" = missing :"Found by bisonex" = missing
    @transform :chrom = missing :pos = missing :ref = missing :alt = missing
    # Rorder
    @select :patient :"transcript (cento)" :"transcript (canonical)" :coding :"genomic (hg38)" :"classification (cento)" :zygosity :gene :"Confirmed in sanger" :"Found by bisonex" :chrom :pos :ref :alt
    # Set -1 for negative variant
    @rtransform :pos = :"transcript (cento)" == "negatif" ? -1 : :pos
    @rtransform :"transcript (canonical)"= :"transcript (cento)" == "negatif" ? "negatif" : :"transcript (canonical)"
    @rtransform :"genomic (hg38)" = :"transcript (cento)" == "negatif" ? "negatif" : :"genomic (hg38)"
    @rtransform :coding = :"transcript (cento)" == "negatif" ? "negatif" : :coding
    @rtransform :gene = :"transcript (cento)" == "negatif" ? "negatif" : :gene
    @rtransform :pos = ismissing(:pos) ? -1 : :pos
    end
CSV.write("variant_extracted_remap.csv", d)
d2 = @chain CSV.read("extracted.csv", DataFrame) begin
    @orderby :patient
    end
CSV.write("extracted_sorted.csv", d2)
#+end_src
ON trie les fichiers pour bien avoir le bon order (sinon diff ne fonctionne pas ??)
diff extracted_sorted.csv variant_extracted_remap.csv  -u | save extracted.diff
 patch -p1 extracted_sorted.csv extracted.diff
patching file extracted_sorted.csv
diff extracted_sorted.csv variant_extracted_remap.csv  -u
**** KILL variant_recoder pour avoir les coordonnées VCF
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
mobidetails n   e trouve pas les ieux transcrits
**** DONE Annotation mobidetails (gene + données gonémique)
CLOSED: [2023-10-25 Wed 09:14]
**** DONE Envoyer liste à Paul
SCHEDULED: <2023-10-26 Thu>
**** DONE compare chaque variant avec la sortie du pipeline
CLOSED: [2023-10-31 Tue 00:18] SCHEDULED: <2023-10-21 Sat>
Avec la fonction "test" dans Search.hs
1126 extracted
654 annotated
253 raw data
102 raw and annotated
236 raw and extracted
17 raw NOT extracted
890 extract WITHOUT raw
#+begin_src sh
❯ open diff.txt | from csv | get id | into string | each {|e| "~/annex/data/centogene/reports/" ++ $e ++ "*.pdf"} | each {|e| firefox $e }
#+end_src
Les 17 manquants sont
- 62913191 : CNV
- 62959388 : MT-ATP6
- 62999572 : MT-ATP6
- 62999627 : CNV
- 62999630 : CNV
- 63004218: CNV
- 63006466 : CNV
- 63009152 : manqué à extraire -> bien présent
- 63015289: CNV
- 63024910 : MT-ATP6
- 63040251 : CNV
- 63043050 : CNV
- 63118093 : NA12878
- NA12878 x4
*** DONE Comparer variants cento à sortie bisonex: 50/121 confirmé en sanger, 71/121 non testé, 0 confirmés manqué par pipeline, 5 manqué mais non confirmés
CLOSED: [2023-11-08 Wed 00:19] SCHEDULED: <2023-11-04 Sat>
*** Comparger sanger : variant seul
Compliqué de reconstituer l'arbre familial. L'information est là mais demande du travail.
ON suppose que le variant n'est que dans la famille....
Résultats
❯ open sa

Insertion in archive/projects.org_archive at line 167 [76.492]

[5.15096]


* DONE Cas clinique H.influenza :hinfluenzae:
CLOSED: [2023-09-28 Thu 11:43]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Finir bibliographie H. influenza
CLOSED: [2023-09-09 Sat 20:19] SCHEDULED: <2023-09-09 Sat>
/Entered on/ [2023-09-09 Sat 16:40]
** DONE Envoyer biblio initiale à Xavier
CLOSED: [2023-09-10 Sun 22:51] SCHEDULED: <2023-09-10 Sun>
** DONE Résumé article PCR
CLOSED: [2023-09-28 Thu 11:43]
/Entered on/ [2023-09-17 Sun 16:08]
** DONE Envoyer première version à Xavier
CLOSED: [2023-09-17 Sun 22:31] SCHEDULED: <2023-09-17 Sun>
/Entered on/ [2023-09-17 Sun 16:08]
* DONE Examen bactério :partiel:
CLOSED: [2023-10-18 Wed 22:52]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Passe 1: tous [37/37]
CLOSED: [2023-10-05 Thu 16:58] DEADLINE: <2023-10-06 Fri> SCHEDULED: <2023-10-06 Fri>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire)>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [X] <(EBCU etiologies)>
  - [X] <(ECBU interpretation)>
  - [X] <(ECBU pre-analytique)>
  - [X] <(EEQ, CIQ)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Hygiène)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes )>
  - [X] <(Pre-analytique bacteriologie)>
  - [X] <(Qualité)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Securite Transfusionnelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [X] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [X] <(Vaccination personnel)>
  - [X]  https://scut.srht.site/notes/medecine/20230528235124-culture.html
  - [X] A. agalactiae
** DONE Passe 2: cours non tobmé avec interro + révision + interro [33/35]
CLOSED: [2023-10-15 Sun 12:59] DEADLINE: <2023-10-11 Wed> SCHEDULED: <2023-10-07 Sat>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [-] Mécanisme résistance antibio
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire)>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [X] <(EBCU etiologies)>
  - [X] <(ECBU interpretation)>
  - [X] <(ECBU pre-analytique)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes)>
  - [X] <(Pre-analytique bacteriologie)>
  - [-] BMR (cours ? définition a minima)
  - [X] <(Qualite)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [X] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [X] <(Culture)>
  - [X] A. agalactiae
** DONE Passe 3 [27/36]
CLOSED: [2023-10-18 Wed 00:10] DEADLINE: <2023-10-16 Mon> SCHEDULED: <2023-10-22 Sun>
  - [X] <(Angines bacteriennes)>
  - [X] <(Antibiogramme - Enterobacteries)>
  - [X] <(Antibiogramme - Staphylocoques)>
  - [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
  - [X] <(Antibiogramme)>
  - [X] <(Cambylobacter)>
  - [ ] Mécanisme résistance antibio
  - [X] <(Chlamydia - mycoplasmes)>
  - [X] <(Clostridium difficile)>
  - [X] <(Concentrations critiques)>
  - [X] <(Conseil anti-infectieux)>
  - [X] <(Declaration obligatoire )>
  - [X] <(Diagnostic moleculaire - Bacteriologie)>
  - [ ] <(EBCU etiologies)>
  - [ ] <(ECBU interpretation)>
  - [ ] <(ECBU pre-analytique)>
  - [X] <(Examen microscopique)>
  - [X] <(Gonocoque)>
  - [X] <(Hemocultures 1)>
  - [X] <(Hemocultures 2)>
  - [X] <(Infections cutanees)>
  - [X] <(Legionelle)>
  - [X] <(MALDI - TOF)>
  - [X] <(Meningites bacteriennes)>
  - [X] <(Pre-analytique bacteriologie)>
  - [ ] BMR (cours ? définition a minima)
  - [X] <(Qualite)>
  - [X] <(Salmonelle - shigelle)>
  - [X] <(Serologie bacterienne)>
  - [X] <(Syphilis)>
  - [X] <(Tests rapides antigeniques et moleculaires)>
  - [ ] <(Tuberculose)>
  - [X] <(Typage moleculaire bacterien)>
  - [ ] <(Culture)>
  - [ ] A. agalactiae
  - [ ] Bactérie (refaire un tour)
* DONE Présentation dépistage hémato :presentation:
CLOSED: [2023-10-19 Thu 18:29]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Refaire analyse bouche
CLOSED: [2023-10-07 Sat 17:49] SCHEDULED: <2023-10-07 Sat>
** DONE Traitement patients bouches
CLOSED: [2023-10-07 Sat 18:01] SCHEDULED: <2023-10-07 Sat>
** DONE Faire analyse selles
CLOSED: [2023-10-07 Sat 19:30] SCHEDULED: <2023-10-07 Sat>
:LOGBOOK:
CLOCK: [2023-10-07 Sat 18:02]--[2023-10-07 Sat 19:30] =>  1:28
:END:
** DONE Revoir avec Audrey pour différence (bleu et jaune)
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Réunion audrey
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Traitement patients selles
CLOSED: [2023-10-10 Tue 22:52] SCHEDULED: <2023-10-09 Mon>
** DONE [#A] Résumer Torres 2022
CLOSED: [2023-10-08 Sun 12:42] SCHEDULED: <2023-10-07 Sat>
<[Pdf]> - "~/papers/bacterio/torres2022.pdf"
<[Notes]> - "~/roam/research/biblio.org#** Multi-body-site colonization screening cultures for predicting multi-drug resistant Gram-negative and Gram-positive bacteremia in hematological patients"
** DONE Première version avec contexte, Torres et nos résultats
CLOSED: [2023-10-11 Wed 21:47] SCHEDULED: <2023-10-08 Sun>
"~/roam/research/presentations/bacterio/depistage hemato/notes.org#* Présentation"
** KILL Présenter Santibiez 2023
CLOSED: [2023-10-19 Thu 18:29]
** DONE Corriger présentation
CLOSED: [2023-10-17 Tue 23:19] SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 22:01]
* DONE Déclaration stage hémato UNESS
CLOSED: [2023-11-14 Tue 22:21] SCHEDULED: <2023-11-13 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer devis dentiste à mutuelle
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-19 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Santé
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-19 Tue 12:18]
* DONE Mail Juliette + Paul pour resoumission
CLOSED: [2023-09-10 Sun 22:36] SCHEDULED: <2023-09-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-10 Sun 22:21]
* DONE Mail Dr Laithier
CLOSED: [2023-09-18 Mon 19:36] SCHEDULED: <2023-09-17 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-17 Sun 16:06]
* DONE Avis paul sur ACPA non
CLOSED: [2023-10-02 Mon 21:58]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Corriger article
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-05 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
** DONE Ajouter images Dr Vidaud
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Comprendre score LRR pour gain
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-21 Thu>
** DONE Corriger discussion: remaniement complexe
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Phénotype "mild" chez le père + détailler moléculaire
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Traitement FBXW7 ?
CLOSED: [2023-10-11 Wed 16:08] SCHEDULED: <2023-10-15 Sun>
Lié à NF1 et non FBXW7 (voir mail V. Laithier)
* DONE Réponse reviewer
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Correction Juliette
CLOSED: [2023-11-18 Sat 11:55] SCHEDULED: <2023-11-19 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Remplacer clavier SK :clavier:
CLOSED: [2023-10-28 Sat 21:36]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-07 Sat 22:58]
** DONE Demande à Cooler Master un remplacement
CLOSED: [2023-10-15 Sun 12:43] SCHEDULED: <2023-10-15 Sun>
Envoyée <2023-10-07 Sat>
Sera probablement refusée car via Amazon
** DONE Retour Amazon
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-28 Sat>
Renvoie vers le constructeur ...
* DONE Coudre fermeture éclair pantalon
CLOSED: [2023-10-11 Wed 12:48] SCHEDULED: <2023-10-11 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-09 Mon 22:09]
* DONE Réclamation train Paris - Besancon
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-22 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-16 Mon 22:01]
** KILL TER
CLOSED: [2023-10-16 Mon 22:05]
"Par ailleurs, en cas de retard ou de suppression de train, il n'existe pas de garantie ponctualité sur TER, aucun remboursement ne sera effectué."
** DONE Allianz
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-23 Mon>
Manque justificatif de retard mais le site ne trouve pas le trajet...
https://www.ter.sncf.com/bourgogne-franche-comte/services-contacts/bulletin-retard-resultats?search=N4IgJgpgDghgTgFwK5wgZQQeygBQDYwDGEIAXKAHYwC2JpIO8AlgM4C0AQhHIQJ4AEHTCgDmmERQj82-Rrxb8wAcgCCSAG7cJJADQhWGbPiJ0EcJBD1MwZEAA4A7ADY7Ttw5B6EvKHRAALViw4JkIQAF89eBD1GDxDXAJiMkoaPy4WGAoAc8wKNgA1JkwEBF19FgTjZNIzCysbekcHAEY7AAZ2jy8fP0CWYNCIqLgYuIARGDLbACZ2mYBmNhb25YBWABVO0m3OgGp5nfbPEGimWLwNplpbFqdSABYPcKA
* DONE Rendre livres BU
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-27 Fri 21:14]
* DONE Changer courroie distribution :courroie:
CLOSED: [2023-09-30 Sat 18:53] SCHEDULED: <2023-09-29 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
À faire au bout de 10ans, on attend l’an prochain
** DONE [#B] Commander pièce
CLOSED: [2023-09-11 Mon 19:18] SCHEDULED: <2023-09-11 Mon>
/Entered on/ [2023-09-11 Mon 19:12]
** DONE Prendre rendez vous
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
* DONE Commander pièce courroie de distribution
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
/Entered on/ [2023-09-11 Mon 19:12]
* DONE Prendre rendez vous courroie distribution
CLOSED: [2023-10-07 Sat 17:48]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
* DONE Changer phare arrière droit
CLOSED: [2023-10-08 Sun 13:24] SCHEDULED: <2023-10-08 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
* DONE Changer ampoule clignotant arrière droit
CLOSED: [2023-10-19 Thu 17:18] SCHEDULED: <2023-10-19 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
Ampoule commandée
* DONE Saisie administrative taxe d'habitation
CLOSED: [2023-07-30 Sun 15:02]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-02 Sun 18:20]
Découverte <2023-07-02 Sun>. Virement 100.50€ fait.
Mail envoyé ce jour
* DONE Vendre
CLOSED: [2023-11-02 Thu 22:31]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
** DONE Envoyer Dimensions frigo et machine à laver
CLOSED: [2023-10-17 Tue 23:20] SCHEDULED: <2023-10-17 Wed>
* DONE Photo à Éric pour lit
CLOSED: [2023-07-30 Sun 19:07] SCHEDULED: <2023-07-30 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
* DONE SMS annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-29 Sat 10:25]
* DONE Lettre recommandée annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
#+category: maison
* DONE Résilier box
CLOSED: [2023-10-26 Thu 09:21] SCHEDULED: <2023-10-26 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-03 Tue 23:11]
Envoyé le mail + règlement intérieur. Ce n'est pas une vrai attestation...
Soit raison impérative (pas de frais), soit logement avec déménagement
* DONE Résilier eau
CLOSED: [2023-11-05 Sun 14:51] SCHEDULED: <2023-11-03 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
À faire après avoir quitté le logement (rétroactif)
* DONE Résilier électricité
CLOSED: [2023-10-26 Thu 09:26] SCHEDULED: <2023-10-26 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
* DONE Résilier ordures ménagères
CLOSED: [2023-10-21 Sat 14:31] SCHEDULED: <2023-10-20 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
Mail envoyé
* DONE Payer ordures ménagères
CLOSED: [2023-10-07 Sat 17:48] SCHEDULED: <2023-10-06 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-03 Tue 23:12]
Envoyé TIP. RIB déjà envoyé ? Sinon à repaer <2023-10-07 Sat>
* DONE Course
CLOSED: [2023-10-09 Mon 22:30] SCHEDULED: <2023-10-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-09 Mon 22:09]
* DONE Renvoyer clavier corsair SK
CLOSED: [2023-10-27 Fri 21:14] SCHEDULED: <2023-10-26 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-26 Thu 09:27]
* DONE Payer facture eau Gennes: à vérifier
CLOSED: [2023-11-10 Fri 16:52] SCHEDULED: <2023-11-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
Payé 2023-11-08, à vérifier
/Entered on/ [2023-11-05 Sun 15:28]
* DONE Déposer chèque caution
CLOSED: [2023-11-10 Fri 16:50] SCHEDULED: <2023-11-07 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-11-06 Mon 21:00]
* KILL Vendre vélo
CLOSED: [2023-11-02 Thu 22:31]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: KILL
:END:
/Entered on/ [2023-07-29 Sat 10:23]
* DONE Demande remboursement frais compte bancaire
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-25 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: banque
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-08-13 Sun 11:16]
À surveiller
Relancé 2023-10-15 Sun: relance la directrice d'agence
* KILL Gentoo package diagrams-graphviz :gentoo:haskell:
CLOSED: [2023-06-24 Sat 15:43] SCHEDULED: <2023-05-28 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Programmation/Gentoo
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: cs
:END:
/Entered on/ [2023-05-27 Sat 22:28]