apraga/org - Change 6XUWY7T2ITWJYRUHDWSG66N7DYCBBXHRHQAAS7GGINDYUJHGMARQC

Notes update

Created by Alexis Praga on October 23, 2022

6XUWY7T2ITWJYRUHDWSG66N7DYCBBXHRHQAAS7GGINDYUJHGMARQC

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In channels

main

Change contents

Replacement in projects.org at line 26 [4.123895]

B:BD[3.2270] → [3.2270:2335]

** [#A] Reddit suggestion
*** TODO Foundational building blocks

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** [#A] [[https://www.reddit.com/r/haskell/comments/npxfba/comment/h084wwa/?utm_source=share&utm_medium=web2x&context=3][Reddit suggestion]]]
*** TODO Learn Foundational building blocks

Replacement in projects.org at line 30 [4.123895]

B:BD[3.2458] → [3.2458:2514]

- [ ] [[https://mmhaskell.com/monads/tutorial][Monads]]

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- [X] [[https://mmhaskell.com/monads/tutorial][Monads]]

Insertion in projects.org at line 37 [4.123895]
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```
**** TODO Look at the example
```

Replacement in projects.org at line 40 [4.123895]

B:BD[3.2805] → [3.2805:3038]

- [ ] Relax for a few days and watch how interactive programs are being
composed
- [ ] Get back to the real-world example and make it a complete
Cabal project.
- [ ] [[https://mmhaskell.com/testing/test-driven-development][Testing]]

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[3.3038]

**** TODO Relax for a few days and watch how interactive programs are being composed
**** TODO Get back to the real-world example and make it a complete Cabal project.
**** TODO [[https://mmhaskell.com/testing/test-driven-development][Testing]]

Deletion in projects.org at line 49 [4.123895]
B:BD[3.4029] → [3.4029:4060]
```
CLOSED: [2022-10-16 Sun 09:41]
```

Replacement in projects.org at line 51 [4.123895]

B:BD[3.4560] → [3.4560:4675]

*** Get back to the real-world example and make it a complete Cabal project.
*** Experiment with various libraires

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*** Experiment with various libraires, read haskell planetarium

Replacement in projects.org at line 61 [4.123895]

B:BD[3.5100] → [3.5100:5198]

**** GHC
***** TODO Lire commentary
***** TODO STRT Lire [[https://www.aosabook.org/en/ghc.html]]

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** GHC
*** TODO GHC commentary
Notamment Ollie Charles's 24 days of GHC Extensions,
*** TODO Lire [[https://www.aosabook.org/en/ghc.html]]
** Vidéos
*** STRT https://www.youtube.com/watch?v=re96UgMk6GQ
** TODO Articles historiques
1. [[https://watermark.silverchair.com/320098.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsYwggLCBgkqhkiG9w0BBwagggKzMIICrwIBADCCAqgGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHXfjdjwhGI2t4bLLAgEQgIICeQjZ-I8gmuaFqBktP4IOifHODtMAHcNF_LwRYyq7NswQ7vT6LJho9P_junCAORLGMV9dgq9JMePH2PFKNxXxrEP1VY7rIDG0gzoeObSkgMDn4MXalrIxD3ejY8vsGYy6vce8Kh70J_UJ8RamO1l3BNNUzy2W6VRaa_cMQr_ekdwcz0oihz0BVKn_bgm_8DjiiPhzj8uU9flVhi13t_oIFA6b3At2QMmPe7Z9OyfLkXivKkmKKNoHwSS7AnTIYAKCO383e4kG6NzZ_elai-XMAJs2Nk0vcgaltld1KeaW3269104DdIlFGevJUVNgwE_4LIheSYRZr9Gr0yRR6TROxdsyxrmgQ22Pzxxpnl8-KdjkW6aRSCKNk_yb5hYcPoRa3ldc5yPV15j8i4t9Mv4U_mBwmIRtMIKPdEHeMvcRx6c8_8uT4RV2esuOPfZlA05bzBgJhMS87M8myxisH-exkTMkm58o6nzHf1lGxzn_JS1VSHbhJCUl82ubzzOWjvl3QJM_vv805XTbn_G-fcRi0d9EQIRTqoObWVFyXW-pz16bWoZPZnBQ1gOmc3hPTGBMZjFR6p9VEAO7bKcK8o0yQDjVWEELNwfAAHc-oF_wLiEjXDNBoUttghgQzzvymKY_jSZhcU8TraVu2i551fpuDNEjSJd0qY5Rg3J6eWU550nJmnoWmX6o7KGiYp0vVMfOoFYXJ1trZWSGoRhDQP2LOLIOt3t2idlj6kV_MoCY3BRnkbxf4XIH7gLJf6Dky6hXFbTU8Fjsn8XHBeKSmaAYJ-sbmGB_BdZO8hHyvHvPv0lTtGcSuKywoJhMbblXRzyuacj_6mZQl5j3tAWhy][Why functional programming matters]]
   Très lisible
2. [[https://dl.acm.org/doi/pdf/10.1145/91556.91592][Comprehending monads]]
   Introduction du concept
3. [[https://dl.acm.org/doi/pdf/10.1145/158511.158524][Imperative functional programming]]
   Application des monads poru résoudre le problème IO

Replacement in projects.org at line 1621 [4.123895]

∅:D[2.98] → [6.172:267]

B:BD[6.172] → [6.172:267]

 - [ ] UTiliser vcfeval pour intersection (permet de gérer les représentations différentes)

[2.98]

[7.14]

 - [ ] Utiliser bcftools isec qui semble faire la même chose que le script d'alexis
   avec option "-c none" "-n~10"

Replacement in projects.org at line 1624 [4.123895]

B:BD[7.15] → [7.15:67]

******* Test: variants dbSNP étiquettés "clinvar"

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******* DONE Test: variants dbSNP étiquettés "clinvar"
CLOSED: [2022-10-23 Sun 18:55]

Replacement in projects.org at line 1635 [4.123895]
B:BD[2.100] → [2.100:129]
```
******* HOLD Essai rtg tools
```
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```
******* DONE Essai rtg tools
CLOSED: [2022-10-23 Sun 13:56]
```
Replacement in projects.org at line 1648 [4.123895]
B:BD[2.691] → [2.691:722]
```
CLOSED: [2022-10-23 Sun 01:05]
```
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```
CLOSED: [2022-10-23 Sun 18:55]
```
Deletion in projects.org at line 1654 [4.123895]
B:BD[2.894] → [2.894:895]

Insertion in projects.org at line 1658 [4.123895]

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#+end_src
******** DONE Impact option -n
CLOSED: [2022-10-23 Sun 13:56]
Mais en spécifiant -n =2:
#+begin_src sh
$ bedtools intersect -a  dbSNP_common.vcf.gz -b clinvar.vcf.gz
74978

Replacement in projects.org at line 1666 [4.123895]

B:BD[2.1024] → [2.1024:1087]

******* DONE bedtools intersect
CLOSED: [2022-10-23 Sun 01:05]

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Si on ne regarde que les variants, on retrouve bien 74302
#+begin_src sh
rg "^NC" none_sorted.vcf  | wc -l
#+end_src
NB : test fait avec
#+begin_src
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | sort > none.vcf
sort common/0003.vcf > common/0003_sorted.vcf
comm -13 common/0003_sorted.vcf none_sorted.vcf
#+end_src
******** DONE Géstion des duplicates: -c none
CLOSED: [2022-10-23 Sun 13:56]
Si on ne garde que ceux avec REF et ALT identiques
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | wc -l
74978
#+end_src
Si on garde tout
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c all -n =2 -w 1 | wc -l
137777
#+end_src
Pour regarder la différence :
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | sort > none_sorted.vcf
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c all -n =2 -w 1 | sort > all_sorted.vcf
comm -13 none_sorted.vcf all_sorted.vcf | head
#+end_src
Sur un exemple,on a bien des variants différents
******** DONE Suppression des clinvar patho
CLOSED: [2022-10-23 Sun 18:55]
Semble faire le travail vu que dbSNP_commo a 23194960 lignes (donc ~80 000 de moins)
 #+begin_src sh
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n~10  dbSNP_common.vcf.gz clinvar.vcf.gz | wc -l
Note: -w option not given, printing list of sites...
23119984
 #+end_src
 Par contre, l'o'ption -w ou -p fait des ficher "data"...
Après un nouvel essai, plus de problème
#+begin_src
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n=1 dbSNP_common.vcf.gz clinvar.vcf.gz -w 1 -o lol.vcf.gz
$ zcat lol.vcf.gz | wc -l
23120660
#+end_src
À noter le choix de l'option -n qui change entre "=1" et "~10"...
En effet "=1" = au moins 1 fichier et "~10" fait exactement dans le premier et non dans le second
#+begin_src
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n~10 dbSNP_common.vcf.gz clinvar.vcf.gz -w 1 -o lol.vcf.gz
$ zcat lol.vcf.gz | wc -l
23120660
#+end_src
******* DONE Essai bedtools intersect

Insertion in projects.org at line 1724 [4.123895]
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```
******* TODO Valider avec Alexis : bcftool isec
```

Insertion in notes/gentoo.org at line 33 [9.75]

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* Difficultés
** ZFS: "Mismatch between pool hostid and system"
zgenhostid $(hostid) résout le problème ?