******* Corriger script alexi
Version initiale
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
    --clinvar $clinvar \
    --chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
    --dbSNP $snp --output tmp.txt
sort tmp.txt > common-notpatho-alexis.txt
wc -l common-notpatho-alexis.txt
#+end_src

#+RESULTS:
: 518832 common-notpatho-alexis.txt
En changeant la condition
#+begin_src sh :dir ~/code/bisonex/test_isec
sed  's/if '\''PATHO'\'' in clinvarline\[7\].upper():/if "Pathogenic" in clinvarline[7]:/' ../script/pythonScript/clinvar_sbSNP.py > ../script/pythonScript/clinvar_sbSNP_patch.py
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP_patch.py \
    --clinvar $clinvar \
    --chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
    --dbSNP $snp --output tmp.txt
sort tmp.txt > common-notpatho-alexis.txt
wc -l common-notpatho-alexis.txt
#+end_src
#+RESULTS:
: 518844 common-notpatho-alexis.txt
Maitenat, 2 de plus que notre version...
#+begin_src sh :dir ~/code/bisonex/test_isec
sort common-notpatho-alexis.txt > sorted.txt
comm -23 sorted.txt common-notpatho-test.txt
#+end_src
#+RESULTS:
| rs3833341  |
| rs73598374 |
rs1799990
rs3833341
rs73598374