apraga/org - Change BKY4GUBANZGG3XDKLMG3HPPAMP457E6JMKTVAZM3RQ4NL5ZKKYSAC

Task update

Created by Alexis Praga on November 23, 2023

BKY4GUBANZGG3XDKLMG3HPPAMP457E6JMKTVAZM3RQ4NL5ZKKYSAC

Dependencies

In channels

main

Change contents

Replacement in projects.org at line 77 [4.123895]
B:BD[3.324] → [2.15:43]
```
SCHEDULED: <2023-11-23 Thu>
```
[3.324]
[3.352]
```
SCHEDULED: <2023-11-24 Fri>
```
Replacement in projects.org at line 93 [4.123895]
B:BD[5.705] → [3.449:482]
```
SCHEDULED: <2023-11-22 Wed .+1d>
```
[5.705]
[5.738]
```
SCHEDULED: <2023-11-24 Fri .+1d>
```
Replacement in projects.org at line 96 [4.123895]
B:BD[5.768] → [3.483:520]
```
:LAST_REPEAT: [2023-11-21 Tue 22:52]
```
[5.768]
[5.805]
```
:LAST_REPEAT: [2023-11-23 Thu 22:13]
```

Replacement in projects.org at line 98 [4.123895]

B:BD[5.811] → [3.521:522]

[5.811]

- State "DONE"       from "TODO"       [2023-11-23 Thu 22:13]
- State "DONE"       from "TODO"       [2023-11-22 Wed 21:33]
- State "DONE"       from "TODO"       [2023-11-21 Tue 21:45]

Deletion in projects.org at line 102 [4.123895]
B:BD[5.873] → [5.873:891]
```
Selfcheck lesson1
```
Replacement in projects.org at line 212 [4.123895]
B:BD[6.356] → [7.207:224]
∅:D[7.224] → [8.190:219]
B:BD[6.373] → [8.190:219]
```
**** DONE Biblio
***** DONE article T. Hirsch
```
[6.356]
[8.219]
```
*** DONE Biblio
CLOSED: [2023-11-23 Thu 21:46]
**** DONE article T. Hirsch
```

Replacement in projects.org at line 216 [4.123895]

B:BD[8.250] → [8.250:303]

***** DONE Autre case report NF1 + hépatoblastome ?

[8.250]

[8.303]

**** DONE Autre case report NF1 + hépatoblastome ?

Replacement in projects.org at line 224 [4.123895]
B:BD[9.1384] → [8.335:367]
```
***** DONE NF1 + autres cancers
```
[9.1384]
[8.367]
```
**** DONE NF1 + autres cancers
```
Replacement in projects.org at line 226 [4.123895]
B:BD[8.398] → [8.398:417]
```
***** DONE Pathway
```
[8.398]
[8.417]
```
**** DONE Pathway
```
Replacement in projects.org at line 254 [4.123895]
∅:D[10.136] → [11.879:892]
∅:D[12.416] → [11.879:892]
B:BD[11.879] → [11.879:892]
```
***** Autres
```
[12.416]
[6.873]
```
**** Autres
```
Replacement in projects.org at line 259 [4.123895]
B:BD[6.962] → [7.225:256]
```
**** KILL Trouver autres cas ?
```
[6.962]
[7.256]
```
*** KILL Trouver autres cas ?
```
Replacement in projects.org at line 261 [4.123895]
B:BD[7.287] → [7.287:316]
```
***** KILL Appel ANDDI rares
```
[7.287]
[7.316]
```
**** KILL Appel ANDDI rares
```
Replacement in projects.org at line 263 [4.123895]
B:BD[7.347] → [7.347:370]
```
***** KILL Appel ITACA
```
[7.347]
[7.370]
```
**** KILL Appel ITACA
```
Replacement in projects.org at line 265 [4.123895]
∅:D[7.401] → [13.1869:1899]
B:BD[6.1045] → [13.1869:1899]
```
**** DONE Plan de l’article
```
[7.401]
[13.1899]
```
*** DONE Plan de l’article
```
Replacement in projects.org at line 267 [4.123895]
B:BD[13.1957] → [8.449:471]
```
**** DONE Poster v0.1
```
[13.1957]
[8.471]
```
*** DONE Poster v0.1
```
Replacement in projects.org at line 269 [4.123895]
B:BD[8.502] → [14.4582:4600]
```
**** DONE Article
```
[8.502]
[14.4600]
```
*** DONE Article
```
Replacement in projects.org at line 271 [4.123895]
∅:D[14.4631] → [7.420:436]
B:BD[7.420] → [7.420:436]
```
***** DONE v0.1
```
[14.4631]
[7.436]
```
**** DONE v0.1
```
Replacement in projects.org at line 273 [4.123895]
B:BD[7.467] → [15.12:40]
```
***** DONE Corrections v0.2
```
[7.467]
[15.40]
```
**** DONE Corrections v0.2
```
Replacement in projects.org at line 275 [4.123895]
B:BD[15.72] → [15.72:116]
```
***** DONE Version validée par paul v0.2.7
```
[15.72]
[15.116]
```
**** DONE Version validée par paul v0.2.7
```
Replacement in projects.org at line 277 [4.123895]
B:BD[15.148] → [16.14:51]
```
***** DONE Correction Hirsch + Vidau
```
[15.148]
[16.51]
```
**** DONE Correction Hirsch + Vidau
```
Replacement in projects.org at line 279 [4.123895]
B:BD[16.110] → [17.252:288]
```
***** DONE Dernières correction JP
```
[16.110]
[17.288]
```
**** DONE Dernières correction JP
```
Replacement in projects.org at line 281 [4.123895]
B:BD[17.347] → [18.1220:1257]
```
***** DONE Relancer avant soumission
```
[17.347]
[18.1257]
```
**** DONE Relancer avant soumission
```
Replacement in projects.org at line 384 [4.123895]
B:BD[5.955] → [5.955:997]
```
*** DONE Implémenter corrections article
```
[5.955]
[5.997]
```
**** DONE Implémenter corrections article
```
Replacement in projects.org at line 386 [4.123895]
∅:D[5.1056] → [19.23688:23689]
∅:D[20.24417] → [19.23688:23689]
B:BD[19.23688] → [19.23688:23689]
B:BD[19.23689] → [5.1057:1113]
B:BD[5.1113] → [3.523:570]
```
*** TODO Correction réponse reviewer +/ article (gain)
SCHEDULED: <2023-11-24 Fri>
*** DONE Mail paul
```
[5.1056]
[2.254]
```
**** TODO Correction réponse reviewer +/ article (gain)
SCHEDULED: <2023-11-23 Thu>
**** DONE Mail paul
```
Replacement in projects.org at line 390 [4.123895]
∅:D[21.71] → [22.560:581]
∅:D[23.159] → [22.560:581]
∅:D[24.187] → [22.560:581]
∅:D[25.241] → [22.560:581]
∅:D[26.269] → [22.560:581]
∅:D[2.313] → [22.560:581]
∅:D[27.538] → [22.560:581]
∅:D[3.629] → [22.560:581]
∅:D[28.730] → [22.560:581]
∅:D[29.813] → [22.560:581]
∅:D[5.1188] → [22.560:581]
∅:D[30.1338] → [22.560:581]
∅:D[31.1902] → [22.560:581]
∅:D[32.3545] → [22.560:581]
B:BD[22.560] → [22.560:581]
```
*** TODO Resoumettre
```
[2.313]
[33.958]
```
**** TODO Resoumettre
```

Insertion in projects.org at line 685 [4.123895]

[5.1350]

[34.1513]

** DONE Réserver location ski
CLOSED: [2023-11-23 Thu 21:45] SCHEDULED: <2023-11-22 Wed>
/Entered on/ [2023-11-22 Wed 22:04]

Deletion in projects.org at line 866 [4.123895]
B:BD[24.553] → [24.553:580]
∅:D[24.580] → [35.3015:3026]
B:BD[35.3015] → [35.3015:3026]
B:BD[35.3026] → [24.581:620]
B:BD[24.620] → [29.943:971]
∅:D[36.145] → [24.648:661]
∅:D[29.971] → [24.648:661]
∅:D[31.2335] → [24.648:661]
∅:D[32.3770] → [24.648:661]
B:BD[24.648] → [24.648:661]
```
- [X] public
- [X] private
- [ ] data
*** TODO depuis raspberry:/media/annex
SCHEDULED: <2023-11-23 Thu>
À vérifier
```
Deletion in projects.org at line 869 [4.123895]
B:BD[24.699] → [24.699:730]
B:BD[24.730] → [29.972:1000]
∅:D[36.174] → [35.3077:3116]
∅:D[24.758] → [35.3077:3116]
∅:D[29.1000] → [35.3077:3116]
∅:D[31.2364] → [35.3077:3116]
∅:D[32.3799] → [35.3077:3116]
B:BD[35.3077] → [35.3077:3116]
```
*** TODO depuis laptop:~/annex
SCHEDULED: <2023-11-23 Thu>
- [ ] public
- [ ] private
- [ ] data
```
Deletion in projects.org at line 883 [4.123895]
B:BD[37.574] → [38.1074:1128]
B:BD[38.1128] → [29.1001:1029]
∅:D[36.203] → [38.1156:1241]
∅:D[29.1029] → [38.1156:1241]
∅:D[31.2393] → [38.1156:1241]
∅:D[32.3828] → [38.1156:1241]
∅:D[14.5147] → [38.1156:1241]
B:BD[38.1156] → [38.1156:1241]
```
** TODO Comprendre pourquoi git-annex ne lit pas home
SCHEDULED: <2023-11-23 Thu>
/Entered on/ [2023-10-01 Sun 21:31]
Unable to parse git config
cannot find git-annex
```

Replacement in projects/bisonex.org at line 2 [40.35]

B:BD[39.5112] → [3.1244:9436]

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: <2023-11-26 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 Venrsion 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: <2023-11-28 Tue>
/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: <2023-11-23 Thu>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-23 Thu>
** 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

[39.5112]

[3.9436]

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: <2023-11-26 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 Venrsion 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: <2023-11-28 Tue>
/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: <2023-11-26 Sun>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-11-26 Sun>
** 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 65 [40.35]

B:BD[3.25822] → [3.25822:33953]

∅:D[3.33953] → [41.51152:51199]

B:BD[41.51152] → [41.51152:51199]

∅:D[41.51199] → [42.93294:93308]

B:BD[42.93294] → [42.93294:93308]

google.com/storage/browser/broad-public-datasets/CHM1_CHM13_WES;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false
*** TODO Télécharger VCF avec nextflow
SCHEDULED: <2023-11-23 Thu>
https://github.com/lh3/CHM-eval/releases
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits ont juste été supprimé
- [X] Erreur de parsing, manque souvent un -
#+begin_src julia
lastTryMobidetails("recoded-failures-mobidetails.csv")
#+end_src
***** DONE Fusionner données
CLOSED: [2023-04-26 Wed 22:35]
#+begin_src julia
function mergeAllGenomic()
    dNew = mergeAll("recoded-success.csv",
                    "recoded-failures-mobidetails.csv",
                    "recoded-failures-mobidetails-redo.csv")
    dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin
        @transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange
        @select :file :transcript :classification :zygosity
        @rename :classificationCento = :classification
    end
    dTmp = outerjoin(dInit, dNew, on = :transcript)
    CSV.write("variant_genomic.csv", dTmp)
end
fSuccess = "recoded-success.csv"
fFailures = "recoded-failures.csv"
# variantRecoder(fSuccess, fFailures)
# mobidetailsOnFailures(fFailures)
# lastTryMobidetails("recoded-failures-mobidetails.csv")
mergeAllGenomic()
#+end_src
***** DONE Formatter donner pour simuscop
CLOSED: [2023-04-28 Fri 11:55] SCHEDULED: <2023-04-26 Wed>
**** KILL Extraire liste des CNVs
CLOSED: [2023-08-12 Sat 15:54]
SCHEDULED: <2023-04-17 Mon>
**** KILL Simuscop :simuscop:
CLOSED: [2023-08-12 Sat 15:54]
***** DONE Entrainer le modèle sur 63003856/
CLOSED: [2023-04-29 Sat 19:56]
Relancer le modèle pour être sûr
***** DONE Générer fastq avec simuscop (del et ins seulement) 20x
CLOSED: [2023-04-28 Fri 23:35] SCHEDULED: <2023-04-22 Sat>
****** DONE Génerer un profile avec bed de centogène
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
NA12878 mais à refaire avec un vrai séquencage
Voir [[*Centogène][Bed Centogène]] pour choix
****** DONE Générer les données en 20x
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
capture de cento
****** DONE Regénérer en supprimant les doublons
CLOSED: [2023-04-28 Fri 17:28]
***** DONE Quelle couverture ?
CLOSED: [2023-04-29 Sat 18:26]
ex sur chr11:16,014,966 où on a 11 reads dans la simulation contre 200 !
****** 200 est la plus proche
#+attr_html: :width 500px
[[./simuscop-200-chr1-1.png]]
#+attr_html: :width 500px
[[./simuscop-200-chr1-2.png]]
****** DONE 20x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 50x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 100x
CLOSED: [2023-04-29 Sat 15:39]
****** DONE 200x
CLOSED: [2023-04-29 Sat 15:39]
***** DONE Reads mal centrés sur des petits exons seuls
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
Capture ok : [[https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A153817168%2D153817824&hgsid=296556270_F4fkENLPXHXidi2oALXls2jxNH9l][UCSC]] (track noire)
Mais mauvaise répartitiopn
#+attr_html: :width 800px
[[./simuscop-error.png]]
À tester
- Problème de profile ?
  - mauvais patient ?
  - mauvaise génération ? -> comparer avec ceux donnés sur github
- nom des chromosomes ?
****** DONE [#A] Tester sur exon 6 GATAD2B pour NC_000001.11:g.153817496A>T
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
******* DONE Configuration + Profile 63003856.profile: idem, mal centré
CLOSED: [2023-04-29 Sat 19:18]
Téléchargement des données
#+begin_src sh :dir ~/code/bisonex/test-simuscop
scp meso:/Work/Projects/bisonex/data/genome/GRCh38.p14/genomeRef.fna .
scp meso:Work/Projects/bisonex/data/simuscop/*.profile .
scp -r meso:/Work/Projects/bisonex/data/genome/GRCh38.p13/bwa .
#+end_src
On récupère l'exon (NB: org-mode ne lance pas le code...)
#+begin_src julia
using CSV,DataFramesMeta
d = CSV.read("VCGS_Exome_Covered_Targets_hg38_40.1MB_renamed.bed", header=false, delim="\t", DataFrame)
@subset d :Column1 .== "NC_000001.11" :Column2 .<= 153817496 :Column3 .>= 153817496
#+end_src
NC_000001.11  153817371  153817542
Génération du bed
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
#+end_src
#+RESULTS:
Génération d'un variant
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "s\tsingle\tNC_000001.11\t153817496\tA\tT\thet"> variant.txt
#+end_src
#+RESULTS:
Génération du fichier de config
#+begin_src sh :dir ~/code/bisonex/test-simuscop
cat > config_wes.txt << EOL
ref = genomeRef.fna
profile = ./63003856.profile
variation = ./variant.txt
target = ./gatad2b-exon6.bed
layout = PE
threads = 1
name = single
output = test-gatad2b
coverage = 20
EOL
#+end_src
#+RESULTS:
On démarre la simulation
#+begin_src sh :dir ~/code/bisonex/test-simuscop
simuReads config_wes.txt
#+end_src
#+RESULTS:
Alignement
#+begin_src sh :dir ~/code/bisonex/test-simuscop
bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:lol\tLB:definition_to_add' bwa/genomeRef test-gatad2b/single_1.fq  test-gatad2b/single_2.fq | samtools sort  -o single.bam
#+end_src
#+RESULTS:
******* DONE Profile github  HiSeq2000
CLOSED: [2023-04-29 Sat 19:56]
#+begin_src sh :dir ~/code/biso
nex/test-simuscop :result file
wget https://ra
w.githubuserco

[3.25822]

[42.93308]

google.com/storage/browser/broad-public-datasets/CHM1_CHM13_WES;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false
*** TODO Télécharger VCF avec nextflow
SCHEDULED: <2023-11-25 Sat>
https://github.com/lh3/CHM-eval/releases
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits ont juste été supprimé
- [X] Erreur de parsing, manque souvent un -
#+begin_src julia
lastTryMobidetails("recoded-failures-mobidetails.csv")
#+end_src
***** DONE Fusionner données
CLOSED: [2023-04-26 Wed 22:35]
#+begin_src julia
function mergeAllGenomic()
    dNew = mergeAll("recoded-success.csv",
                    "recoded-failures-mobidetails.csv",
                    "recoded-failures-mobidetails-redo.csv")
    dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin
        @transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange
        @select :file :transcript :classification :zygosity
        @rename :classificationCento = :classification
    end
    dTmp = outerjoin(dInit, dNew, on = :transcript)
    CSV.write("variant_genomic.csv", dTmp)
end
fSuccess = "recoded-success.csv"
fFailures = "recoded-failures.csv"
# variantRecoder(fSuccess, fFailures)
# mobidetailsOnFailures(fFailures)
# lastTryMobidetails("recoded-failures-mobidetails.csv")
mergeAllGenomic()
#+end_src
***** DONE Formatter donner pour simuscop
CLOSED: [2023-04-28 Fri 11:55] SCHEDULED: <2023-04-26 Wed>
**** KILL Extraire liste des CNVs
CLOSED: [2023-08-12 Sat 15:54]
SCHEDULED: <2023-04-17 Mon>
**** KILL Simuscop :simuscop:
CLOSED: [2023-08-12 Sat 15:54]
***** DONE Entrainer le modèle sur 63003856/
CLOSED: [2023-04-29 Sat 19:56]
Relancer le modèle pour être sûr
***** DONE Générer fastq avec simuscop (del et ins seulement) 20x
CLOSED: [2023-04-28 Fri 23:35] SCHEDULED: <2023-04-22 Sat>
****** DONE Génerer un profile avec bed de centogène
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
NA12878 mais à refaire avec un vrai séquencage
Voir [[*Centogène][Bed Centogène]] pour choix
****** DONE Générer les données en 20x
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
capture de cento
****** DONE Regénérer en supprimant les doublons
CLOSED: [2023-04-28 Fri 17:28]
***** DONE Quelle couverture ?
CLOSED: [2023-04-29 Sat 18:26]
ex sur chr11:16,014,966 où on a 11 reads dans la simulation contre 200 !
****** 200 est la plus proche
#+attr_html: :width 500px
[[./simuscop-200-chr1-1.png]]
#+attr_html: :width 500px
[[./simuscop-200-chr1-2.png]]
****** DONE 20x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 50x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 100x
CLOSED: [2023-04-29 Sat 15:39]
****** DONE 200x
CLOSED: [2023-04-29 Sat 15:39]
***** DONE Reads mal centrés sur des petits exons seuls
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
Capture ok : [[https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A153817168%2D153817824&hgsid=296556270_F4fkENLPXHXidi2oALXls2jxNH9l][UCSC]] (track noire)
Mais mauvaise répartitiopn
#+attr_html: :width 800px
[[./simuscop-error.png]]
À tester
- Problème de profile ?
  - mauvais patient ?
  - mauvaise génération ? -> comparer avec ceux donnés sur github
- nom des chromosomes ?
****** DONE [#A] Tester sur exon 6 GATAD2B pour NC_000001.11:g.153817496A>T
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
******* DONE Configuration + Profile 63003856.profile: idem, mal centré
CLOSED: [2023-04-29 Sat 19:18]
Téléchargement des données
#+begin_src sh :dir ~/code/bisonex/test-simuscop
scp meso:/Work/Projects/bisonex/data/genome/GRCh38.p14/genomeRef.fna .
scp meso:Work/Projects/bisonex/data/simuscop/*.profile .
scp -r meso:/Work/Projects/bisonex/data/genome/GRCh38.p13/bwa .
#+end_src
On récupère l'exon (NB: org-mode ne lance pas le code...)
#+begin_src julia
using CSV,DataFramesMeta
d = CSV.read("VCGS_Exome_Covered_Targets_hg38_40.1MB_renamed.bed", header=false, delim="\t", DataFrame)
@subset d :Column1 .== "NC_000001.11" :Column2 .<= 153817496 :Column3 .>= 153817496
#+end_src
NC_000001.11  153817371  153817542
Génération du bed
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
#+end_src
#+RESULTS:
Génération d'un variant
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "s\tsingle\tNC_000001.11\t153817496\tA\tT\thet"> variant.txt
#+end_src
#+RESULTS:
Génération du fichier de config
#+begin_src sh :dir ~/code/bisonex/test-simuscop
cat > config_wes.txt << EOL
ref = genomeRef.fna
profile = ./63003856.profile
variation = ./variant.txt
target = ./gatad2b-exon6.bed
layout = PE
threads = 1
name = single
output = test-gatad2b
coverage = 20
EOL
#+end_src
#+RESULTS:
On démarre la simulation
#+begin_src sh :dir ~/code/bisonex/test-simuscop
simuReads config_wes.txt
#+end_src
#+RESULTS:
Alignement
#+begin_src sh :dir ~/code/bisonex/test-simuscop
bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:lol\tLB:definition_to_add' bwa/genomeRef test-gatad2b/single_1.fq  test-gatad2b/single_2.fq | samtools sort  -o single.bam
#+end_src
#+RESULTS:
******* DONE Profile github  HiSeq2000
CLOSED: [2023-04-29 Sat 19:56]
#+begin_src sh :dir ~/code/bisonex/test-simuscop :result file
wget https://raw.githubuserco

Insertion in archive/projects.org_archive at line 762 [44.492]

[43.61091]


* KILL depuis raspberry:/media/annex
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups/Git-annex en local
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
À vérifier
- [X] public
- [X] private
- [ ] data
* KILL depuis laptop:~/annex
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups/Git-annex en local
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
- [ ] public
- [ ] private
- [ ] data

Insertion in archive/projects.org_archive at line 792 [44.492]

[43.61092]

* KILL Comprendre pourquoi git-annex ne lit pas home
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
/Entered on/ [2023-10-01 Sun 21:31]
Unable to parse git config
cannot find git-annex
* KILL Comprendre pourquoi git-annex ne lit pas home
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
/Entered on/ [2023-10-01 Sun 21:31]
Unable to parse git config
cannot find git-annex

Task update

Dependencies

In channels

Change contents

Replacement in projects.org at line 77 [4.123895]

Replacement in projects.org at line 93 [4.123895]

Replacement in projects.org at line 96 [4.123895]

Replacement in projects.org at line 98 [4.123895]

Deletion in projects.org at line 102 [4.123895]

Replacement in projects.org at line 212 [4.123895]

Replacement in projects.org at line 216 [4.123895]

Replacement in projects.org at line 224 [4.123895]

Replacement in projects.org at line 226 [4.123895]

Replacement in projects.org at line 254 [4.123895]

Replacement in projects.org at line 259 [4.123895]

Replacement in projects.org at line 261 [4.123895]

Replacement in projects.org at line 263 [4.123895]

Replacement in projects.org at line 265 [4.123895]

Replacement in projects.org at line 267 [4.123895]

Replacement in projects.org at line 269 [4.123895]

Replacement in projects.org at line 271 [4.123895]

Replacement in projects.org at line 273 [4.123895]

Replacement in projects.org at line 275 [4.123895]

Replacement in projects.org at line 277 [4.123895]

Replacement in projects.org at line 279 [4.123895]

Replacement in projects.org at line 281 [4.123895]

Replacement in projects.org at line 384 [4.123895]

Replacement in projects.org at line 386 [4.123895]

Replacement in projects.org at line 390 [4.123895]

Insertion in projects.org at line 685 [4.123895]

Deletion in projects.org at line 866 [4.123895]

Deletion in projects.org at line 869 [4.123895]

Deletion in projects.org at line 883 [4.123895]

Replacement in projects/bisonex.org at line 2 [40.35]

Replacement in projects/bisonex.org at line 65 [40.35]

Insertion in archive/projects.org_archive at line 762 [44.492]

Insertion in archive/projects.org_archive at line 792 [44.492]