apraga/org - Change LDUJHWYYQXZPU2O2ND4SLAZXJWFS3YLCIR7CWOWYMC7DM3P5AHEAC

Workout, cooking, bacterio

Created by Alexis Praga on May 2, 2023

LDUJHWYYQXZPU2O2ND4SLAZXJWFS3YLCIR7CWOWYMC7DM3P5AHEAC

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main

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Insertion in workout.org at line 6186 [3.1]

[2.73]

* <2023-05-02 Tue> Workout
** RTO
- 28
- 13
- 13
** L-sit
3x1
** Muscle-up
- 3x1 + 4 neg
- 3+1 (!) + 4 neg
- 3+1 (!) + 4 neg
** Extension:
3x22
** FL tucked row :
- 3+2
- 3+2
- 3+2
** Pistols :
3x4
** Planche tucked push-up:
- 3x3+1
- 3x3+1
- 4+4+2
** Compression:
-3x10
** Norwegian roll
- 3x4

Replacement in projects/bisonex.org at line 43 [4.35]

B:BD[2.377394] → [2.377394:384270]


26×10 DataFrame
 Row │ chrom         pos       variant        variantType  zygosity      ref        alt        refCount  altCount  readsCount
     │ SubStrin…?    Int64     SubStrin…?     String?      String15      SubStrin…  SubStrin…  Int64     Int64     Int64
─────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1 │ NC_000015.10  74343027  g.74343027C>T  snv          heterozygous  C          T                61        58         120
   2 │ NC_000015.10  75400778  g.75400778C>G  snv          heterozygous  C          G               108        79         187
   3 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
   4 │ NC_000015.10  48767448  g.48767448A>C  snv          heterozygous  A          C                72        70         142
   5 │ NC_000015.10  75411685  g.75411685T>C  snv          heterozygous  T          C                79        81         160
   6 │ NC_000015.10  66703292  g.66703292C>T  snv          heterozygous  C          T                70        60         130
   7 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
   8 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
   9 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
  10 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
  11 │ NC_000015.10  42401752  g.42401752G>A  snv          homozygous    G          A                61       212         273
  12 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
  13 │ NC_000015.10  38339896  g.38339896G>A  snv          heterozygous  G          A                56        86         144
  14 │ NC_000015.10  26869324  g.26869324A>T  snv          heterozygous  A          T                62        49         113
  15 │ NC_000015.10  66435145  g.66435145G>A  snv          heterozygous  G          A                98        95         193
  16 │ NC_000015.10  60514655  g.60514655G>A  snv          heterozygous  G          A                94        99         194
  17 │ NC_000015.10  42410947  g.42410947A>G  snv          heterozygous  A          G               153       123         276
  18 │ NC_000015.10  75430368  g.75430368C>T  snv          heterozygous  C          T                80        62         142
  19 │ NC_000015.10  25375494  g.25375494T>C  snv          heterozygous  T          C               103       104         207
  20 │ NC_000015.10  60497497  g.60497497C>A  snv          heterozygous  C          A                61        65         126
  21 │ NC_000015.10  74891539  g.74891539C>T  snv          heterozygous  C          T               118       124         242
  22 │ NC_000015.10  48488433  g.48488433A>G  snv          heterozygous  A          G               367       122         492
  23 │ NC_000015.10  89318565  g.89318565A>G  snv          heterozygous  A          G               303        98         404
  24 │ NC_000015.10  89323426  g.89323426C>G  snv          heterozygous  C          G                93       109         202
  25 │ NC_000015.10  89318595  g.89318595T>C  snv          heterozygous  T          C               321       128         453
  26 │ NC_000015.10  48488437  g.48488437T>C  snv          heterozygous  T          C               356       132         488
CLOSED: [2023-05-01 Mon 17:18]
***** TODO Chromosome1 15 :Test haplotype caller : échec
SCHEDULED: <2023-05-01 Mon>
#+begin_src
julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` 63003856_S135_chr15_inserted.bam
scp 63003856_S135_chr15_inserted.bam* meso:/Work/Users/apraga/bisonex/tests/synthetic/
#+end_src
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/synthetic :results silent
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .
#+end_src
puis
#+begin_src
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output testchr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10
#+end_src
scp meso:/Work/Users/apraga/bisonex/tests/synthetic/testchr15.vcf.gz haplotypecaller-chr15.vcf.gz
Aucun variant inséré
- base quality ok
  -
****** DONE bam out : non appelé
CLOSED: [2023-05-01 Mon 21:57]
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.f
na  --tmp-dir . -L NC_000015.10  --bam-output debug.bam
****** DONE --linked-de-bruijn-graph : idem
CLOSED: [2023-05-01 Mon 21:57]
readlink testchr15.vcf.gz -f^C
[apraga@mesointeractive synthetic]$ gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10  --linked-de-bruijn-graph
****** TODO regénérer fastq
***** TODO Générer bam données pour tous les chromosomes
 timeit julia -Jbisonex.so --project=. insertVariants.jl ~/code/bisonex/out/63003856/preprocessing/63003856_S135.bam 63003856_S135_inserted.bam
40min 516ms 835µs 405ns
Avertissement:
 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Inserted.bam et excluded.bam (fichier avant le merge)  ont l'air ok...
On réessaie à la main : ça passe
#+begin_src
samtools merge test-all.bam inserted.bam excluded.bam
❯ mv test-all.bam `63003856_S135_inserted.bam` -f
❯ mv test-all.bam.bai `63003856_S135_chr15_inserted.bam.bai` -f
#+end_src
***** TODO BAm2fastq
SCHEDULED: <2023-05-01 Mon>
 scp 63003856_S135_chr15_inserted.bam* meso:/Work/Groups/bisonex/data/synthetic/
***** TODO Lancer pipeline
SCHEDULED: <2023-05-01 Mon>
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]
* DONE Plot : ashkenazim trio
CLOSED: [2023-04-18 Tue 21:28] SCHEDULED: <2023-04-16 Sun>
/Entered on/ [2023-04-16 Sun 17:29]

[2.377394]


26×10 DataFrame
 Row │ chrom         pos       variant        variantType  zygosity      ref        alt        refCount  altCount  readsCount
     │ SubStrin…?    Int64     SubStrin…?     String?      String15      SubStrin…  SubStrin…  Int64     Int64     Int64
─────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1 │ NC_000015.10  74343027  g.74343027C>T  snv          heterozygous  C          T                61        58         120
   2 │ NC_000015.10  75400778  g.75400778C>G  snv          heterozygous  C          G               108        79         187
   3 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
   4 │ NC_000015.10  48767448  g.48767448A>C  snv          heterozygous  A          C                72        70         142
   5 │ NC_000015.10  75411685  g.75411685T>C  snv          heterozygous  T          C                79        81         160
   6 │ NC_000015.10  66703292  g.66703292C>T  snv          heterozygous  C          T                70        60         130
   7 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
   8 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
   9 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
  10 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
  11 │ NC_000015.10  42401752  g.42401752G>A  snv          homozygous    G          A                61       212         273
  12 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
  13 │ NC_000015.10  38339896  g.38339896G>A  snv          heterozygous  G          A                56        86         144
  14 │ NC_000015.10  26869324  g.26869324A>T  snv          heterozygous  A          T                62        49         113
  15 │ NC_000015.10  66435145  g.66435145G>A  snv          heterozygous  G          A                98        95         193
  16 │ NC_000015.10  60514655  g.60514655G>A  snv          heterozygous  G          A                94        99         194
  17 │ NC_000015.10  42410947  g.42410947A>G  snv          heterozygous  A          G               153       123         276
  18 │ NC_000015.10  75430368  g.75430368C>T  snv          heterozygous  C          T                80        62         142
  19 │ NC_000015.10  25375494  g.25375494T>C  snv          heterozygous  T          C               103       104         207
  20 │ NC_000015.10  60497497  g.60497497C>A  snv          heterozygous  C          A                61        65         126
  21 │ NC_000015.10  74891539  g.74891539C>T  snv          heterozygous  C          T               118       124         242
  22 │ NC_000015.10  48488433  g.48488433A>G  snv          heterozygous  A          G               367       122         492
  23 │ NC_000015.10  89318565  g.89318565A>G  snv          heterozygous  A          G               303        98         404
  24 │ NC_000015.10  89323426  g.89323426C>G  snv          heterozygous  C          G                93       109         202
  25 │ NC_000015.10  89318595  g.89318595T>C  snv          heterozygous  T          C               321       128         453
  26 │ NC_000015.10  48488437  g.48488437T>C  snv          heterozygous  T          C               356       132         488
CLOSED: [2023-05-01 Mon 17:18]
***** TODO Chromosome1 15 :Test haplotype caller : échec car CIGARE non mis à jour
SCHEDULED: <2023-05-01 Mon>
#+begin_src
julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` 63003856_S135_chr15_inserted.bam
scp 63003856_S135_chr15_inserted.bam* meso:/Work/Users/apraga/bisonex/tests/synthetic/
#+end_src
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/synthetic :results silent
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .
#+end_src
puis
#+begin_src
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output testchr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10
#+end_src
scp meso:/Work/Users/apraga/bisonex/tests/synthetic/testchr15.vcf.gz haplotypecaller-chr15.vcf.gz
Aucun variant inséré
- base quality ok
  -
****** DONE bam out : non appelé
CLOSED: [2023-05-01 Mon 21:57]
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.f
na  --tmp-dir . -L NC_000015.10  --bam-output debug.bam
****** DONE --linked-de-bruijn-graph : idem
CLOSED: [2023-05-01 Mon 21:57]
readlink testchr15.vcf.gz -f^C
[apraga@mesointeractive synthetic]$ gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10  --linked-de-bruijn-graph
****** HOLD regénérer fastq
***** TODO Générer bam données pour tous les chromosomes
 timeit julia -Jbisonex.so --project=. insertVariants.jl ~/code/bisonex/out/63003856/preprocessing/63003856_S135.bam 63003856_S135_inserted.bam
40min 516ms 835µs 405ns
Avertissement:
 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Inserted.bam et excluded.bam (fichier avant le merge)  ont l'air ok...
On réessaie à la main : ça passe
#+begin_src
samtools merge test-all.bam inserted.bam excluded.bam
❯ mv test-all.bam `63003856_S135_inserted.bam` -f
❯ mv test-all.bam.bai `63003856_S135_chr15_inserted.bam.bai` -f
#+end_src
***** TODO BAm2fastq pour avoir CIGAR à jour
SCHEDULED: <2023-05-01 Mon>
 rsync -avz 63003856_S135_inserted.bam* meso:/Work/Groups/bisonex/data/synthetic/
***** TODO Lancer pipeline
SCHEDULED: <2023-05-01 Mon>
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]
* DONE Plot : ashkenazim trio
CLOSED: [2023-04-18 Tue 21:28] SCHEDULED: <2023-04-16 Sun>
/Entered on/ [2023-04-16 Sun 17:29]

Replacement in notes/cooking.org at line 224 [3.590656]

B:BD[3.598413] → [3.598413:598480]

** diviser quantité par 2 : brownie fin dans un plat à tarte. **

[3.598413]

[3.598480]

*** diviser quantité par 2 : brownie fin dans un plat à tarte. **

Insertion in notes/cooking.org at line 243 [3.590656]

[3.599390]


** TODO Cookies
https://www.seriouseats.com/the-food-lab-best-chocolate-chip-cookie-recipe
*** Ingredients
    8 ounces unsalted butter (2 sticks; 225g)
    1 standard ice cube (about 2 tablespoons; 30mL frozen water)
    10 ounces all-purpose flour (about 2 cups; 280g)
    3/4 teaspoon (3g) baking soda
    2 teaspoons Diamond Crystal kosher salt or 1 teaspoon table salt (4g)
    5 ounces granulated sugar (about 3/4 cup; 140g)
    2 large eggs (100g)
    2 teaspoons (10mL) vanilla extract
    5 ounces dark brown sugar (about 1/2 tightly packed cup plus 2 tablespoons; 140g)
    8 ounces (225g) semisweet chocolate, roughly chopped with a knife into 1/2- to 1/4-inch chunks
    Coarse sea salt, for garnish
*** Recette
10-11min cuisson 180

Insertion in notes/cooking.org at line 261 [3.590656]
[3.599391]
[3.599391]

File addition: bacteriologie.org (----------)

[5.29]

* PCR 16s
Gène /16s/ code sous-unité 16s de l'ADN ribosomal -> très conservé dans toutes les bactéries
Sert à identifier la présence de bactéries +/- espèce par analyse du code génétique si une seule bactérie
* Résistances
** Staph aureus
Sensibile aux pénicillines mais 90% sont résistantes à la pénicilline G  (sécrétion d'une pénicillisanes).
Ils restent sensibles à la pénicilline M = /méti-S/
Attention: < 20% ont résistance à toutes les beta-lactamines ! (modification de la cible = protéine de liaison à la pénicilline PLP2A) ->
/meti-R/ (SARM)
** Entérobactéries
Résistantes aux beta-lactamine par production de beta-lactamase