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gad-public
pharmAnnot
Commits
be49ef4b
Commit
be49ef4b
authored
Aug 24, 2018
by
Simon Verdez
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ccub
parent
95e566f2
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3 changed files
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3 additions
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3 deletions
+3
-3
Master.sh
Master.sh
+2
-2
VCF_tools.pyc
VCF_tools.pyc
+0
-0
create_html.py
create_html.py
+1
-1
No files found.
Master.sh
View file @
be49ef4b
...
@@ -115,7 +115,7 @@ echo "Start : $(date +"%F_%H-%M-%S")"
...
@@ -115,7 +115,7 @@ echo "Start : $(date +"%F_%H-%M-%S")"
for
currentSample
in
$samples
for
currentSample
in
$samples
do
do
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"
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
-hold_jid
varcallCNV_
${
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
-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"
)
"
...
@@ -126,6 +126,6 @@ echo "Start : $(date +"%F_%H-%M-%S")"
...
@@ -126,6 +126,6 @@ echo "Start : $(date +"%F_%H-%M-%S")"
for
currentSample
in
$samples
for
currentSample
in
$samples
do
do
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"
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
.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
-
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
done
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
VCF_tools.pyc
View file @
be49ef4b
No preview for this file type
create_html.py
View file @
be49ef4b
...
@@ -141,7 +141,7 @@ for record in vcf_reader_SNP.fetch():
...
@@ -141,7 +141,7 @@ for record in vcf_reader_SNP.fetch():
body
=
body
.
append
(
htmltag
.
P
(
htmltag
.
P2
(
"pathologie: "
+
patho
))
+
htmltag
.
P
(
htmltag
.
P2
(
"molecule: "
+
molecule
))
+
htmltag
.
P
(
htmltag
.
P2
(
"gene: "
+
gene
.
encode
(
'utf-8'
)))
+
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
(
"pathologie: "
+
patho
))
+
htmltag
.
P
(
htmltag
.
P2
(
"molecule: "
+
molecule
))
+
htmltag
.
P
(
htmltag
.
P2
(
"gene: "
+
gene
.
encode
(
'utf-8'
)))
+
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
))))
body
=
body
.
append
(
htmltag
.
P
(
htmltag
.
P2
(
htmltag
.
A
(
href
=
publi
)
.
append
(
"publication: "
+
publi
))))
else
:
else
:
body
=
body
.
append
(
htmltag
.
P
(
"pathologie: "
+
patho
)
+
htmltag
.
P
(
"molecule: "
+
molecule
)
+
htmltag
.
P
(
"gene: "
+
gene
.
encode
(
'utf-8'
))
+
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
(
"pathologie: "
+
patho
)
+
htmltag
.
P
(
"molecule: "
+
molecule
)
+
htmltag
.
P
(
"gene: "
+
gene
.
encode
(
'utf-8'
)
+
type
(
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
(
htmltag
.
A
(
href
=
publi
)
.
append
(
"publication: "
+
publi
)))
body
=
body
.
append
(
htmltag
.
P
(
"#######################################################################"
))
body
=
body
.
append
(
htmltag
.
P
(
"#######################################################################"
))
except
:
except
:
...
...
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