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Commit 3c5a5a82 authored by Simon Verdez's avatar Simon Verdez
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pipeline works

parent 5f8e477e
master dev public
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Showing with 321 additions and 10 deletions
Master.sh
View file @ 3c5a5a82
...@@ -66,7 +66,7 @@ PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2` ...@@ -66,7 +66,7 @@ PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2`
OMIM=`grep "omim" $PHARMCONFIG | cut -f2` OMIM=`grep "omim" $PHARMCONFIG | cut -f2`
HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2` HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2`
HEADER=`grep "header" $PHARMCONFIG | cut -f2` HEADER=`grep "header" $PHARMCONFIG | cut -f2`
REF=`grep "reference" $PHARMCONFIG | cut -f2`
# python path for proper execution of python # python path for proper execution of python
PYTHONPATH=$PIPELINEBASE/common:/work/gad/shared/bin/lib/python_2.7/lib/python2.7/site-packages:/work/gad/shared/bin/miniconda2/lib/python2.7/site-packages/ PYTHONPATH=$PIPELINEBASE/common:/work/gad/shared/bin/lib/python_2.7/lib/python2.7/site-packages:/work/gad/shared/bin/miniconda2/lib/python2.7/site-packages/
...@@ -104,11 +104,11 @@ else ...@@ -104,11 +104,11 @@ else
fi fi
# get the status # get the status
REF=`grep "reference" $STATUSFILE | cut -f2`
HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2` HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2`
varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2` varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2`
varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2` varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2`
createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2` createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2`
mergeVCF=`grep "mergeVCF" $STATUSFILE | cut -f2`
if [ "$HLAscan" == "FAIL" ] if [ "$HLAscan" == "FAIL" ]
then then
...@@ -139,6 +139,14 @@ else ...@@ -139,6 +139,14 @@ else
echo "CreateHTML step was OK" echo "CreateHTML step was OK"
fi fi
if [ "$mergeVCF" == "FAIL" ]
then
echo "MergeVCF step failed : jumping to merge step"
jumpto MergeVCF
else
echo "MerfeVCF step was OK"
fi
echo "pipeline was correctly executed, no need to relaunch a step" echo "pipeline was correctly executed, no need to relaunch a step"
exit 0 exit 0
fi fi
...@@ -172,7 +180,7 @@ echo "### Execute HLAscan ###" ...@@ -172,7 +180,7 @@ echo "### Execute HLAscan ###"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,OUTPUTFILE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh" echo "Command : qsub -pe smp 2 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,OUTPUTFILE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh"
qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v BAM=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,SORTIE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v BAM=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,SORTIE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh
done done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
...@@ -208,8 +216,8 @@ echo "### Generate HTML report ###" ...@@ -208,8 +216,8 @@ echo "### Generate HTML report ###"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh" echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh"
qsub -pe smp 1 -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCFFILE_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCFFILE_CNV=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/$currentSample.report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh
done done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
...@@ -219,7 +227,7 @@ echo "### Merge VCF files" ...@@ -219,7 +227,7 @@ echo "### Merge VCF files"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh" echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh"
qsub -pe smp 1 -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh
done done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
create_html.py 0 → 100755
View file @ 3c5a5a82
#!/usr/bin/python
### PharmAnnot PIPELINE ###
## create_html_v2.py
## Version : 1.0.0
## Description : Create a html file with vcf file, BAM file and report HLAscan
## Usage : python create_html_v2.py -v vcf_SNP -c vcf_CNV -h report_HLA -b BAM -t tsvfile -o html -e log
## Output : Annotated vcf file
## Requirements : python 2.7+
## Author : Simon.Verdez@u-bourgogne.fr
## Creation Date : 20180731
## last revision date : 20180731
## Known bugs : None
#Example : python create_html_v2.py dijex2000.vcf report_HLA BAM
import sys
import getopt
import subprocess
import csv
from pysam import VariantFile
import htmltag
import logging
from operator import *
# Options
try:
opts, args = getopt.getopt(sys.argv[1:], 'v:c:h:b:t:o:e')
for opt, arg in opts:
if opt in ("-v"):
vcfSNP = arg
if opt in ("-c"):
vcfCNV = arg
if opt in ("-h"):
report = arg
if opt in ("-b"):
bam = arg
if opt in ("-t"):
tsvfile = arg
elif opt in ("-o"):
sys.stdout = open(arg, 'w')
elif opt in ("-e"):
logfile = arg
except getopt.GetoptError:
print 'usage : '
sys.exit(1)
# Logging
logging.basicConfig(filename = '%s' % (logfile), filemode = 'a', level = logging.INFO, format = '%(asctime)s %(levelname)s - %(message)s')
logging.info('start')
# Manage options
if not vars().has_key('vcfSNP'):
logging.exception('No vcf SNP file given')
sys.exit(1)
if not vars().has_key('vcfCNV'):
logging.exception('No vcf CNV file given')
sys.exit(1)
if not vars().has_key('report'):
logging.exception('No report HLAscan given')
sys.exit(1)
if not vars().has_key('bam'):
logging.exception('No bam file given')
sys.exit(1)
if not vars().has_key('tsvfile'):
logging.exception('No tsv file given')
sys.exit(1)
# Check files
try:
f = open(vcfSNP, 'r')
f.close()
except IOError:
logging.exception('vcfSNP file does not exist')
sys.exit(1)
try:
f = open(vcfCNV, 'r')
f.close()
except IOError:
logging.exception('vcfCNV file does not exist')
sys.exit(1)
try:
f = open(report, 'r')
f.close()
except IOError:
logging.exception('Report HLAscan file does not exist')
sys.exit(1)
try:
f = open(bam, 'r')
f.close()
except IOError:
logging.exception('BAM file does not exist')
sys.exit(1)
try:
f = open(tsvfile, 'r')
f.close()
except IOError:
logging.exception('Tsv file does not exist')
sys.exit(1)
""" construction du formulaire en premier"""
head = htmltag.HEAD()
head = htmltag.append(htmltag.TITLE('pharmacogenetic'))
head = head.append(htmltag.STYLE(type="text/css").append("body { padding-left: 15em; font-family: Georgia; color:black }"))
head = head.append(htmltag.STYLE(type="text/css").append("h2 { padding-left: 15em;font-family: Georgia;color:blue }"))
head = head.append(htmltag.STYLE(type="text/css").append("ul.navbar { list-style-type: none; padding: 0; margin: 0; position: absolute; top: 2em; left: 1em; width: 13em }"))
head = head.append(htmltag.STYLE(type="text/css").append("ul.navbar li { background: yellow; margin: 0.5em 0; padding: 1em; border-left: 0.5em solid black }"))
head = head.append(htmltag.STYLE(type="text/css").append("P1 {color: red }"))
head = head.append(htmltag.STYLE(type="text/css").append("P2 { color: orange }"))
body = htmltag.BODY()
body = body.append(htmltag.UL(CLASS = "navbar").append(htmltag.UL(htmltag.LI(htmltag.A(href = "https://www.pharmgkb.org").append("pharmgkb")))).append(htmltag.UL(htmltag.LI(htmltag.A(href = "https://cpicpgx.org").append("cpicpgx")))).append(htmltag.UL(htmltag.LI(htmltag.A(href = "http://www.pharmacogenetics.fr/").append("pharmacogenetics.fr")))))
body = body.append(htmltag.H2('Variants pharmgkb'))
"""extraction des donnees """
data = tsvfile
vcf_reader_SNP = VariantFile(vcfSNP)
vcf_reader_CNV = VariantFile(vcfCNV)
BAM_FILE = bam
Report_HLA = open(report,"r")
for record in vcf_reader_SNP.fetch():
try:
for i in range(len(record.info["Pharmaco_Annot"])/12):
try:
gene = repr(record.info["GENEINFO"])
except:
gene = "intron"
alt = record.info["Pharmaco_Annot"][(i*12)+1].replace(")","").replace("'","").replace("-","")
pheno = record.info["Pharmaco_Annot"][(i*12)+3].replace(")","").replace("'","").replace("-"," ")
publi = record.info["Pharmaco_Annot"][(i*12)+5].replace(")","").replace("'","").replace("-"," ")
level = record.info["Pharmaco_Annot"][(i*12)+7].replace(")","").replace("'","").replace("-","")
patho = record.info["Pharmaco_Annot"][(i*12)+9].replace(")","").replace("'","").replace("-","")
molecule = record.info["Pharmaco_Annot"][(i*12)+11].replace(")","").replace("'","").replace("-"," ").replace("]","")
if level.startswith("1"):
body= body.append(htmltag.P(htmltag.P1("pathologie: "+patho))+htmltag.P(htmltag.P1("molecule: "+molecule))+htmltag.P(htmltag.P1("gene: "+gene))+htmltag.P(htmltag.P1("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id)))+htmltag.P(htmltag.P1("base alternative: "+alt))+htmltag.P(htmltag.P1("niveau: "+level))+htmltag.P(htmltag.P1("phenotype: "+pheno)))
body= body.append(htmltag.P(htmltag.P1(htmltag.A(href = publi).append("publication: "+publi))))
elif level.startswith("2"):
body= body.append(htmltag.P(htmltag.P2("pathologie: "+patho))+htmltag.P(htmltag.P2("molecule: "+molecule))+htmltag.P(htmltag.P2("gene: "+gene))+htmltag.P(htmltag.P2("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id)))+htmltag.P(htmltag.P2("base alternative: "+alt))+htmltag.P(htmltag.P2("niveau: "+level))+htmltag.P(htmltag.P2("phenotype: "+pheno)))
body= body.append(htmltag.P(htmltag.P2(htmltag.A(href = publi).append("publication: "+publi))))
else :
body= body.append(htmltag.P("pathologie: "+patho)+htmltag.P("molecule: "+molecule)+htmltag.P("gene: "+gene)+htmltag.P("variant: "+repr(record.pos)+" "+repr(record.ref)+">"+repr(record.alts)+" "+repr(record.id))+htmltag.P("base alternative: "+alt)+htmltag.P("niveau: "+level)+htmltag.P(htmltag.P("phenotype: "+pheno)))
body= body.append(htmltag.P(htmltag.A(href = publi).append("publication: "+publi)))
body= body.append(htmltag.P("#######################################################################"))
except:
pass
body = body.append(htmltag.H2('Deletion ou duplication'))
for record in vcf_reader_CNV.fetch():
for elm in record.alts:
if elm == "<DEL>":
ListeM = []
ListeD = []
body= body.append(htmltag.P("Deletion detectee par xHMM sur le gene "+record.info["GENE"]))
with open(data) as tsvfile:
reader = csv.DictReader(tsvfile, dialect='excel-tab')
for row in reader:
if row['gene'] != "":
if row['drug'] == record.info["GENE"]:
if row['drug'] not in ListeM:
ListeG.append(row['drug'])
for Mol in ListeM:
body= body.append(htmltag.P("######Gene ayant une relation avec :"+Mol))
depth_ave = 0.0
pos_len = 0
depth_new = 0
p = subprocess.Popen(["samtools", 'depth', BAM_FILE, '-r', record.chrom + ':' + str(record.pos) + '-'\
+ str(record.stop)], stdout = subprocess.PIPE)
for line in p.stdout.readlines():
item = line.split()
if len(item) == 3:
ListeD.append(item[2])
for elm in ListeD:
depth_new = depth_new + int(elm)
depth_ave = depth_ave + float(item[2])
pos_len = pos_len + (int(record.stop) - int(record.pos) + 1)
depth_ave = depth_new/float(pos_len)
if depth_ave > 40:
body= body.append(htmltag.P("######Detecte heterozygote, profondeur moyenne :"+str(depth_ave)))
if depth_ave < 10:
body= body.append(htmltag.P("######Detecte homozygote, profondeur moyenne :"+str(depth_ave)))
else:
body= body.append(htmltag.P("######Detecte probablement heterozygote, profondeur moyenne :"+str(depth_ave)))
if elm == "<DUP>":
ListeM = []
body= body.append(htmltag.P("Duplication detectee par xHMM sur le gene "+record.info["GENE"]))
with open(data) as tsvfile:
reader = csv.DictReader(tsvfile, dialect='excel-tab')
for row in reader:
if row['gene'] != "":
if row['drug'] == record.info["GENE"]:
if row['drug'] not in ListeM:
ListeG.append(row['drug'])
for Mol in ListeM:
body= body.append(htmltag.P("######Gene ayant une relation avec :"+Mol))
HLA = Report_HLA.readlines()
ListeA = []
ListeB = []
ListeC = []
ListeDQB1 = []
ListeDRB1 = []
for lines in HLA :
if lines.startswith("A"):
for ligne in lines.split("\t"):
if ligne.startswith("A*"):
ListeA.append(ligne)
if lines.startswith("B"):
for ligne in lines.split("\t"):
if ligne.startswith("B*"):
ListeB.append(ligne)
if lines.startswith("C"):
for ligne in lines.split("\t"):
if ligne.startswith("C*"):
ListeC.append(ligne)
if lines.startswith("DQB1"):
for ligne in lines.split("\t"):
if ligne.startswith("DQB1*"):
ListeDQB1.append(ligne)
if lines.startswith("DRB1"):
for ligne in lines.split("\t"):
if ligne.startswith("DRB1*"):
ListeDRB1.append(ligne)
body = body.append(htmltag.H2('Resultat genotypage HLA'))
body = body.append(htmltag.P("HLA-A : "+ListeA[0]+" / "+ListeA[1]))
body = body.append(htmltag.P("HLA-B : "+ListeB[0]+" / "+ListeB[1]))
body = body.append(htmltag.P("HLA-C : "+ListeC[0]+" / "+ListeC[1]))
body = body.append(htmltag.P("HLA-DQB1 : "+ListeDQB1[0]+" / "+ListeDQB1[1]))
body = body.append(htmltag.P("HLA-DRB1 : "+ListeDRB1[0]+" / "+ListeDRB1[1]))
with open(data) as tsvfile:
reader = csv.DictReader(tsvfile, dialect='excel-tab')
for row in reader:
if row['gene'] != "":
if row['variants'].startswith("HLA-A"):
Adigit = row['variants'].split("*")[1]
Adigit2 = Adigit.split(":")[0]+Adigit.split(":")[1]
HL1 = ListeA[0].split("*")[1].split(":")[0]+ListeA[0].split("*")[1].split(":")[1]
HL2 = ListeA[1].split("*")[1].split(":")[0]+ListeA[1].split("*")[1].split(":")[1]
if HL1 == Adigit2:
pheno = row['effect']
publi = row['article']
level = str(row['LEVEL'])
if level.startswith("1"):
body = body.append(htmltag.P1(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if level.startswith("2"):
body = body.append(htmltag.P2(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
else:
body = body.append(htmltag.P(pheno)+htmltag.P(level))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if HL2 == Adigit2:
pheno = row['effect']
publi = row['article']
level = str(row['LEVEL'])
if level.startswith("1"):
body = body.append(htmltag.P1(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if level.startswith("2"):
body = body.append(htmltag.P2(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
else:
body = body.append(htmltag.P(pheno)+htmltag.P(level))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if row['variants'].startswith("HLA-B"):
Bdigit = row['variants'].split("*")[1]
Bdigit2 = Bdigit.split(":")[0]+Bdigit.split(":")[1]
HL1 = ListeB[0].split("*")[1].split(":")[0]+ListeB[0].split("*")[1].split(":")[1]
HL2 = ListeB[1].split("*")[1].split(":")[0]+ListeB[1].split("*")[1].split(":")[1]
if HL1 == Bdigit2:
pheno = row['effect']
publi = row['article']
level = str(row['LEVEL'])
if level.startswith("1"):
body = body.append(htmltag.P1(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if level.startswith("2"):
body = body.append(htmltag.P2(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P2(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
else:
body = body.append(htmltag.P(pheno)+htmltag.P(level))
body = body.append(htmltag.P(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if HL2 == Bdigit2:
pheno = row['effect']
publi = row['article']
level = str(row['LEVEL'])
if level.startswith("1"):
body = body.append(htmltag.P1(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P1(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
if level.startswith("2"):
body = body.append(htmltag.P2(htmltag.P(pheno)+htmltag.P(level)))
body = body.append(htmltag.P2(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
else:
body = body.append(htmltag.P(pheno)+htmltag.P(level))
body = body.append(htmltag.P(htmltag.P(htmltag.A(href = publi).append("publication: "+publi))))
print htmltag.HTML(head+body)
merge_GATK.sh
View file @ 3c5a5a82
...@@ -81,10 +81,10 @@ fi ...@@ -81,10 +81,10 @@ fi
JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}') JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}') PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}')
GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}') #GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
echo "command : $JAVA -jar $GATK -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY" echo "command : $JAVA -jar /work/gad/shared/bin/GATK_3.8/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY"
$JAVA -jar $GATK -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE $JAVA -jar /work/gad/shared/bin/GATK_3.8/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE
genotypeMerge_exitcode=$? genotypeMerge_exitcode=$?
echo "GenotypeMerge exit code : $genotypeMerge_exitcode" echo "GenotypeMerge exit code : $genotypeMerge_exitcode"
......
pharmconfig.tsv
View file @ 3c5a5a82
...@@ -3,3 +3,4 @@ pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf ...@@ -3,3 +3,4 @@ pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
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