apraga/org - Change ZV5YCHTZKVBL5ZW7NIQZLI5W6KEXSQ3T4XQNAPUQPJV2OJ6CKNLQC

Saving tasks

Created by Alexis Praga on November 5, 2023

ZV5YCHTZKVBL5ZW7NIQZLI5W6KEXSQ3T4XQNAPUQPJV2OJ6CKNLQC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 6794 [6.1]

[5.150]

* <2023-11-04 Sat> Workout
Plus espacés, sur arbre (nouveau logement)
** RTO 10
- 10-10-10
- 10-10-10
- 10-10-10
** L-sit
- 1
- 1
** Muscle-up
-  1-1-1
-  1-1-1
-  1-1
-  1-1-1
-  1-1-1
** Pistols :
- 4
- 4
- 4
- 4
- 4

Replacement in projects.org at line 60 [6.123895]

∅:D[4.104] → [7.14:140]

∅:D[8.129] → [7.14:140]

∅:D[9.156] → [7.14:140]

∅:D[10.296] → [7.14:140]

∅:D[11.348] → [7.14:140]

∅:D[12.363] → [7.14:140]

∅:D[13.374] → [7.14:140]

∅:D[14.508] → [7.14:140]

B:BD[15.1219] → [7.14:140]

∅:D[16.42] → [7.168:186]

B:BD[7.168] → [7.168:186]

B:BD[7.187] → [17.14:99]

∅:D[17.99] → [18.173:209]

B:BD[18.173] → [18.173:209]

∅:D[7.187] → [19.14:132]

∅:D[18.209] → [19.14:132]

B:BD[15.1219] → [19.14:132]

∅:D[20.42] → [21.187:223]

∅:D[22.71] → [21.187:223]

∅:D[19.132] → [21.187:223]

B:BD[21.187] → [21.187:223]

** Logement trevenans :trevenans:cs:
*** DONE Compléter dossier
CLOSED: [2023-08-30 Wed 16:38]
*** TODO Assurance habitation
Attente décision
*** DONE Louer camionette
CLOSED: [2023-09-16 Sat 18:19] SCHEDULED: <2023-09-16 Sat>
/Entered on/ [2023-09-13 Wed 22:57]
** DONE Copie carte d'identié + mutuelle accueil hôpital
CLOSED: [2023-08-19 Sat 20:09] SCHEDULED: <2023-08-17 Thu>
/Entered on/ [2023-08-08 Tue 21:18]

[4.104]

[16.43]

** Logement trevenans :trevenans:
*** WAIT Assurance habitation
    SCHEDULED: <2023-11-12 Sun>
    Attente décision
*** DONE Envoyer état des lieux
    CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
*** DONE Envoyer papiers : clé, wifi, autorisation accès
    CLOSED: [2023-11-05 Sun 15:10] SCHEDULED: <2023-11-05 Sun>
    /Entered on/ [2023-11-05 Sun 14:55]
*** TODO Demander pour ouverture de ligne
    SCHEDULED: <2023-11-05 Sun>
    /Entered on/ [2023-11-05 Sun 14:56]
*** TODO Arrêter résilier et souscrire nouveau contrat :internet:
SCHEDULED: <2023-11-13 Mon>
Appel 2023-11-03: ouverture nouvelle ligne dans 9 jours
RV demain

Deletion in projects.org at line 213 [6.123895]

B:BD[3.129] → [3.129:290]

∅:D[3.290] → [23.69:98]

B:BD[23.69] → [23.69:98]

B:BD[23.98] → [3.291:422]

** TODO Arrêter résilier et souscrire nouveau contrat :internet:
SCHEDULED: <2023-11-13 Mon>
Appel 2023-11-03: ouverture nouvelle ligne dans 9 jours
RV demain
** TODO Assurance habitation
SCHEDULED: <2023-11-03 Fri>
*** DONE Mail coloc pour discuter assurance
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>

Deletion in projects.org at line 245 [6.123895]

∅:D[24.345] → [25.183:319]

B:BD[26.4581] → [25.183:319]

B:BD[25.319] → [27.224:359]

B:BD[27.359] → [28.15:116]

∅:D[28.116] → [29.336:397]

B:BD[29.336] → [29.336:397]

B:BD[29.397] → [3.423:639]

** DONE Dossier admnistratatif Trevenans
CLOSED: [2023-10-09 Mon 22:30] SCHEDULED: <2023-10-09 Mon>
/Entered on/ [2023-10-09 Mon 22:08]
** DONE Envoyer choix d'option précoce
CLOSED: [2023-10-10 Tue 23:12] SCHEDULED: <2023-10-10 Tue>
/Entered on/ [2023-10-10 Tue 23:12]
** DONE Demande de conservation de compte
CLOSED: [2023-10-22 Sun 21:06] SCHEDULED: <2023-10-20 Fri>
/Entered on/ [2023-10-19 Thu 18:27]
Nécessite UF (demandé)
** DONE Relancer DAM pour conservation compte
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>
** DONE Mail DSI pour conservation compte (attente)
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>

Replacement in projects.org at line 538 [6.123895]
∅:D[30.43] → [10.454:489]
∅:D[31.452] → [10.454:489]
∅:D[3.668] → [10.454:489]
∅:D[32.1757] → [10.454:489]
∅:D[16.2530] → [10.454:489]
∅:D[33.3371] → [10.454:489]
B:BD[10.454] → [10.454:489]
B:BD[10.489] → [3.669:697]
```
**** TODO Ajouter images Dr Vidaud
SCHEDULED: <2023-11-05 Sun>
```
[3.668]
[10.517]
```
**** DONE Ajouter images Dr Vidaud
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
```
Replacement in projects.org at line 542 [6.123895]
∅:D[10.617] → [34.266:318]
B:BD[34.266] → [34.266:318]
B:BD[34.318] → [3.698:726]
∅:D[35.72] → [34.407:475]
∅:D[36.154] → [34.407:475]
∅:D[37.541] → [34.407:475]
∅:D[10.646] → [34.407:475]
∅:D[3.726] → [34.407:475]
∅:D[14.1022] → [34.407:475]
∅:D[32.1815] → [34.407:475]
∅:D[16.2588] → [34.407:475]
∅:D[33.3429] → [34.407:475]
∅:D[38.7727] → [34.407:475]
B:BD[34.407] → [34.407:475]
B:BD[34.475] → [3.727:755]
```
**** TODO Corriger discussion: remaniement complexe
SCHEDULED: <2023-11-05 Sun>
**** TODO Phénotype "mild" chez le père + détailler moléculaire
SCHEDULED: <2023-11-05 Sun>
```
[10.617]
[39.522]
```
**** 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>
```
Replacement in projects.org at line 549 [6.123895]
∅:D[39.659] → [31.453:480]
∅:D[33.3487] → [31.453:480]
B:BD[8.158] → [31.453:480]
B:BD[31.480] → [3.756:784]
```
*** TODO Réponse reviewer
SCHEDULED: <2023-11-05 Sun>
```
[39.659]
[31.481]
```
*** DONE Réponse reviewer
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
```
Replacement in projects.org at line 552 [6.123895]
B:BD[31.510] → [3.785:813]
```
SCHEDULED: <2023-11-05 Sun>
```
[31.510]
[34.560]
```
SCHEDULED: <2023-11-12 Sun>
```
Replacement in projects.org at line 856 [6.123895]
B:BD[39.793] → [30.73:101]
```
SCHEDULED: <2023-11-01 Wed>
```
[39.793]
[39.821]
```
SCHEDULED: <2023-11-06 Mon>
```
Replacement in projects.org at line 931 [6.123895]
∅:D[40.533] → [41.1983:2005]
B:BD[13.461] → [41.1983:2005]
B:BD[41.2005] → [30.263:291]
```
** TODO Résilier eau
SCHEDULED: <2023-11-03 Fri>
```
[40.533]
[30.291]
```
** DONE Résilier eau
CLOSED: [2023-11-05 Sun 14:51] SCHEDULED: <2023-11-03 Fri>
```

Insertion in projects.org at line 949 [6.123895]

[30.539]

[20.72]

** TODO Payer facture eau Gennes
SCHEDULED: <2023-11-19 Sun>
/Entered on/ [2023-11-05 Sun 15:28]

Replacement in projects/bisonex.org at line 2 [43.35]

B:BD[42.5112] → [3.1045:9237]

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 T2T
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** TODO Mise à jour packages nix
*** TODO Corriger PR
SCHEDULED: <2023-11-05 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: <2023-11-03 Fri>
/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: <2023-11-06 Mon>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-06 Mon>
** 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
*** D

[42.5112]

[3.9237]

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:
*** TODO Corriger PR
SCHEDULED: <2023-11-05 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: <2023-11-03 Fri>
/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: <2023-11-06 Mon>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-06 Mon>
** 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
*** D

Insertion in inbox.org at line 2 [45.197]

[44.152]

* TODO Envoyer papiers : clé, wifi, autorisation accès
/Entered on/ [2023-11-05 Sun 14:55]

Insertion in archive/projects.org_archive at line 22 [2.492]

[2.1006]

:END:
* DONE Compléter dossier
CLOSED: [2023-08-30 Wed 16:38]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat/Logement trevenans
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: trevenans cs
:END:
* DONE Louer camionette
CLOSED: [2023-09-16 Sat 18:19] SCHEDULED: <2023-09-16 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat/Logement trevenans
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: trevenans cs
:END:
/Entered on/ [2023-09-13 Wed 22:57]
* DONE Mail DSI pour conservation compte (attente)
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Relancer DAM pour conservation compte
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Demande de conservation de compte
CLOSED: [2023-10-22 Sun 21:06] SCHEDULED: <2023-10-20 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-19 Thu 18:27]
Nécessite UF (demandé)
* DONE Envoyer choix d'option précoce
CLOSED: [2023-10-10 Tue 23:12] SCHEDULED: <2023-10-10 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-10 Tue 23:12]
* DONE Dossier admnistratatif Trevenans
CLOSED: [2023-10-09 Mon 22:30] SCHEDULED: <2023-10-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-09 Mon 22:08]
* DONE Présentation dépistage hémato :presentation:
CLOSED: [2023-10-19 Thu 18:29]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
: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 Cas clinique H.influenza :hinfluenzae:
CLOSED: [2023-09-28 Thu 11:43]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
: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 Copie carte d'identié + mutuelle accueil hôpital
CLOSED: [2023-08-19 Sat 20:09] SCHEDULED: <2023-08-17 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE

Insertion in archive/projects.org_archive at line 166 [2.492]
[2.1012]
```
/Entered on/ [2023-08-08 Tue 21:18]
```

Saving tasks

Dependencies

In channels

Change contents

Insertion in workout.org at line 6794 [6.1]

Replacement in projects.org at line 60 [6.123895]

Deletion in projects.org at line 213 [6.123895]

Deletion in projects.org at line 245 [6.123895]

Replacement in projects.org at line 538 [6.123895]

Replacement in projects.org at line 542 [6.123895]

Replacement in projects.org at line 549 [6.123895]

Replacement in projects.org at line 552 [6.123895]

Replacement in projects.org at line 856 [6.123895]

Replacement in projects.org at line 931 [6.123895]

Insertion in projects.org at line 949 [6.123895]

Replacement in projects/bisonex.org at line 2 [43.35]

Insertion in inbox.org at line 2 [45.197]

Insertion in archive/projects.org_archive at line 22 [2.492]

Insertion in archive/projects.org_archive at line 166 [2.492]