apraga/org - Change E22LJP4FLYXYGD3WCHOV64RX6H3MOTKQV3ZBZOBWBON6CTL64CCAC

Bisonex, books, workout

Created by Alexis Praga on February 3, 2023

E22LJP4FLYXYGD3WCHOV64RX6H3MOTKQV3ZBZOBWBON6CTL64CCAC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 5780 [4.1]

[3.276]

* <2023-02-03 Fri> Workout
- RTO: 20-10-10
Skin-the-cat (avec descente): 2-2
- Muscle-up 3x1 - 2+1+1 - 2+1+1+1
Extension: 3x22
- FL tucked row : 3x{3+2}
Pistols : 3x4
- Planche tucked push-up: 3x{6+4} !
Compression: 3x9

Replacement in projects/bisonex.org at line 832 [6.35]
B:BD[5.315] → [3.290:320]
```
**** DONE Version par défaut
```
[5.315]
[3.320]
```
**** DONE Version sans rtgtools avec python 3
```

Replacement in projects/bisonex.org at line 841 [6.35]

B:BD[3.718] → [3.718:751]

**** TODO Version avec rtg-tools

[3.718]

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**** DONE Version avec python3
CLOSED: [2023-02-04 Sat 00:25]
**** TODO Sérialiser json pour écrire données de sorties
**** DONE Tester sur example
CLOSED: [2023-02-04 Sat 00:25]
#+begin_src sh
$ cd hap.py
$ ../result/bin/hap.py example/happy/PG_NA12878_chr21.vcf.gz       example/happy/NA12878_chr21.vcf.gz       -f example/happy/PG_Conf_chr21.bed.gz       -o test -r example/chr21.fa
#+end_src
#+RESULTS:
| 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    |        8937 |     7839 |     1098 |       11812 |      343 |      3520 |    45 |   283 |      0.877140 |         0.958635 |       0.298002 |        0.916079 |                    NaN |                    NaN |                  1.357991 |                  1.457627 |   |
| INDEL | PASS   |        8937 |     7550 |     1387 |        9971 |      283 |      1964 |    30 |   242 |      0.844803 |         0.964656 |       0.196971 |        0.900760 |                    NaN |                    NaN |                  1.357991 |                  1.239305 |   |
| SNP   | ALL    |       52494 |    52125 |      369 |       90092 |      582 |     37348 |   107 |   354 |      0.992971 |         0.988966 |       0.414554 |        0.990964 |               2.082614 |               1.745874 |                  1.594335 |                  3.132586 |   |
| SNP   | PASS   |       52494 |    46920 |     5574 |       48078 |      143 |       992 |     8 |    97 |      0.893816 |         0.996963 |       0.020633 |        0.942576 |               2.082614 |               2.089282 |                  1.594335 |                  1.487599 |   |
**** TODO Version avec rtg-tools |

Replacement in projects/bisonex.org at line 2720 [6.35]

B:BD[5.449] → [5.449:623]

$ ${HAPPY}/bin/hap.py  \
      example/happy/PG_NA12878_chr21.vcf.gz \
      example/happy/NA12878_chr21.vcf.gz \
      -f example/happy/PG_Conf_chr21.bed.gz \
      -o test

[5.449]

[3.800]

Télécharger :
#+begin_src

Insertion in projects/bisonex.org at line 2728 [6.35]
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[3.1296]
```
#+end_src
```

Replacement in projects/bisonex.org at line 2730 [6.35]

B:BD[3.1297] → [3.1297:1598]

 HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna ./result/bin/hap.py script/files/vcf/NA12878_NIST7035_vep_annot.vcf /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -f /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test

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Renommer chromosomes sur BED
#+begin_src
sed -i.bak \
-e 's/chr1/NC_000001.11/' \
-e 's/chr2/NC_000002.12/' \
-e 's/chr3/NC_000003.12/' \
-e 's/chr4/NC_000004.12/' \
-e 's/chr5/NC_000005.10/' \
-e 's/chr6/NC_000006.12/' \
-e 's/chr7/NC_000007.14/' \
-e 's/chr8/NC_000008.11/' \
-e 's/chr9/NC_000009.12/' \
-e 's/chr10/NC_000010.11/' \
-e 's/chr11/NC_000011.10/' \
-e 's/chr12/NC_000012.12/' \
-e 's/chr13/NC_000013.11/' \
-e 's/chr14/NC_000014.9/' \
-e 's/chr15/NC_000015.10/' \
-e 's/chr16/NC_000016.10/' \
-e 's/chr17/NC_000017.11/' \
-e 's/chr18/NC_000018.10/' \
-e 's/chr19/NC_000019.10/' \
-e 's/chr20/NC_000020.11/' \
-e 's/chr21/NC_000021.9/' \
-e 's/chr22/NC_000022.11/' \
-e 's/chrX/NC_000023.11/' \
-e 's/chrY/NC_000024.10/' \
-e 's/chrMT/NC_012920.1/' /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed \
#+end_src
et sur vcf
#+begin_src
awk '{print "chr"$2" "$1}' /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping.txt > /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping_reverse.txt
bcftools annotate --rename-chrs /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping_reverse.txt /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz  -o /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark_renam
ed.vcf.gz
#+end_src
HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna ./result/bin/hap.py /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1
_benchmark_renamed.vcf.gz script/files/vcf/NA12878_NIST7035_vep_annot.vcf -f /Work/Groups/bison
ex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test

Insertion in notes/nix.org at line 245 [10.47]

[9.245]

** Vérifier les dépendences à l'exécution
Il faut les mettre dans propagatedBuildInputs (buildInputs ne suffit pas). On vérifie avec :
#+begin_src sh
$ nix-instantiate -E "with import <nixpkgs> {}; callPackage pkgs/hap-py.nix {}"
/nix/store/scbx1aiadh24qwwjhskp7jdqngsm31x7-hap.py.drv
$ nix-store -r /nix/store/scbx1aiadh24qwwjhskp7jdqngsm31x7-hap.py.drv
(...installation...)
/nix/store/kgxqmk7jdi91jwbrj4qz5q5c4qhh8qzb-hap.py
$ nix-store -q --references /nix/store/kgxqmk7jdi91jwbrj4qz5q5c4qhh8qzb-hap.py
#+end_src
Si le program en a besoin, wrapper le programme en rajoutant dans nativeBuildInputs makeWrapper :
#+begin_src sh
  nativeBuildInputs = [ pkgs.makeWrapper ];
  postBuild = with lib; with pkgs; ''
    wrapProgram $out/bin/test.sh\
      --prefix PATH : ${makeBinPath [ bcftools samtools]}
  '';
}
#+end_src

Insertion in notes/music.org at line 5 [4.139882]

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** TODO Vol. 02 Sacred Cantatas: 11/15
** TODO Vol. 03 Sacred Cantatas: 0/15
** TODO Vol. 04 Sacred Cantatas: 0/15
** TODO Vol. 05 Secular Cantatas: 0/11
** TODO Vol. 06 Sacred Vocal Works: 0/14
** TODO Vol. 07 Motets, Chorales, Songs: 01/07
** TODO Vol. 08 Organ Works: 0/16
** TODO Vol. 09 Keyboard Works I: 0/11
** TODO Vol. 10 Keyboard works II: 0/11
** TODO Vol. 11 Chamber Music: 1/13
** TODO Vol. 12 Concertos, Orchestral Suites: 0/10

Deletion in notes/music.org at line 17 [4.139882]

B:BD[4.139953] → [4.139953:140385]

- TODO Vol. 02 Sacred Cantatas: 11/15
- TODO Vol. 03 Sacred Cantatas: 0/15
- TODO Vol. 04 Sacred Cantatas: 0/15
- TODO Vol. 05 Secular Cantatas: 0/11
- TODO Vol. 06 Sacred Vocal Works: 0/14
- TODO Vol. 07 Motets, Chorales, Songs: 01/07
- TODO Vol. 08 Organ Works: 0/16
- TODO Vol. 09 Keyboard Works I: 0/11
- TODO Vol. 10 Keyboard works II: 0/11
- TODO Vol. 11 Chamber Music: 1/13
- TODO Vol. 12 Concertos, Orchestral Suites: 0/10

Replacement in notes/music.org at line 336 [4.139882]

B:BD[2.140] → [2.140:213]

- [ ] Abdullah Ibrahim - Yarona - 1995 (CD - FLAC - Lossless)-158236.tor

[2.140]

[2.213]

- [X] Abdullah Ibrahim - Yarona - 1995 (CD - FLAC - Lossless)-158236.tor

Replacement in notes/books.org at line 96 [4.675275]

B:BD[11.1420] → [12.1578:1595]

** STRT Rabelais

[11.1420]

** HOLD Rabelais
*** DONE Gargantua
*** DONE Pantagruel
*** DONE Tiers livre
CLOSED: [2023-02-03 Fri 21:45]