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pharmAnnot
Commit 5f8e477e authored by Simon Verdez's avatar Simon Verdez
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ccub_test

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Master.sh
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VCF_tools.pyc 0 → 100644
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File added
analysis_config.tsv 0 → 100755
View file @ 5f8e477e
pipelinebase /work/gad/shared/pipeline/pharmacogen_test/pharmAnnot
pythonbin /work/gad/shared/bin/miniconda2/bin/python
GATKbase /work/gad/shared/bin/GATK_3.7
javacmd /soft/java/jdk_x64/bin/java
picardbase /work/gad/shared/bin/PICARD_2.4.1
temporary_dir /work/gad/shared/tmp/
reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
refdict /work/gad/shared/pipeline/hg19/index/hg19_essential.dict
refdir /work/gad/shared/pipeline/hg19/index
dbsnp /work/gad/shared/pipeline/hg19/clinvar/dbsnp.vcf
mainqueue batch
autosubqueue batchbm
bwacmd /work/gad/shared/bin/bwa-0.7.15
fastqccmd /work/gad/shared/bin/FastQC_0.11.4/fastqc
fastqc_config /work/gad/shared/bin/FastQC_0.11.4/Configuration/limits.txt
trimmomatic /work/gad/shared/bin/Trimmomatic-0.35/trimmomatic-0.35.jar
adapters_file /work/gad/shared/bin/Trimmomatic-0.35/adapters/TruSeq3-PE-All.fa
samtools /work/gad/shared/bin/samtools-1.5/
igvtools /work/gad/shared/bin/IGVTools_2.3.67/igvtools.jar
targetlist /work/gad/shared/pipeline/hg19/targets/
refseqlist /work/gad/shared/pipeline/hg19/refseq/refseq.cds.2bp.hg19.with_genes.interval_list
refseqgenelist /work/gad/shared/pipeline/hg19/refseq/genetrack.hg19.sorted.refseq
controlfile /work/gad/shared/pipeline/samples/control_100_samples.g.vcf
email emilie.tisserant@u-bourgogne.fr
clinvar_vcf /work/gad/shared/pipeline/hg19/clinvar/clinvar.vcf
cosmic_vcf /work/gad/shared/pipeline/hg19/cosmic/CosmicCodingMuts.vcf
omim_list /work/gad/shared/pipeline/hg19/omim/OMIM2.list
acmg_list /work/gad/shared/pipeline/hg19/omim/ACMG.list
common_list /work/gad/shared/pipeline/hg19/clinvar/common.list
ssa_nb_files 10
tabixpath /work/gad/shared/bin/htslib-1.3/bin/tabix
kaviar /work/gad/shared/pipeline/hg19/kaviar/Kaviar-160204-Public-hg19.vcf.gz
regulomedb /work/gad/shared/pipeline/hg19/regulomeDB/RegulomeDB.dbSNP141.txt.gz
targetscan /work/gad/shared/pipeline/hg19/targetscan/Predicted_Targets.hg19.bed
cytobands /work/gad/shared/pipeline/hg19/cnv/cytobands.tsv
dgv_variants /work/gad/shared/pipeline/hg19/cnv/GRCh37_hg19_variants_2015-07-23.txt.gz
cnv_map /work/gad/shared/pipeline/hg19/cnv/Stringent.hg19.2015-02-03.txt.gz
isca_benign_cnv /work/gad/shared/pipeline/hg19/cnv/iscaBenign.txt.gz
isca_pathogenic_cnv /work/gad/shared/pipeline/hg19/cnv/iscaPathogenic.txt.gz
devdelay_control_cnv /work/gad/shared/pipeline/hg19/cnv/cnvDevDelayControl.txt.gz
devdelay_case_cnv /work/gad/shared/pipeline/hg19/cnv/cnvDevDelayCase.txt.gz
clingen_dosage_sensitive_gene /work/gad/shared/pipeline/hg19/cnv/ClinGen_gene_curation_list.tsv
xhmmbin /work/gad/shared/bin/xhmm_1.0/xhmm
xhmmparams /work/gad/shared/pipeline/hg19/cnv/xhmm_params.txt
cnvtarget /work/gad/shared/pipeline/hg19/cnv/cnv_targets_refseq_only_coding_exon_2bp.hg19.list
targetgc /work/gad/shared/pipeline/hg19/cnv/cnv_targets_refseq_only_coding_exon_2bp.hg19_GC.txt
docmatrix /work/gad/shared/pipeline/hg19/cnv/ALL.CNV.RD.txt
extremegc /work/gad/shared/pipeline/hg19/cnv/extreme_gc_targets.txt
lowcomplexity /work/gad/shared/pipeline/hg19/cnv/low_complexity_targets.txt
controlfreec /work/gad/shared/bin/ControlFreeC
gemMappabilityFile /work/gad/shared/pipeline/hg19/cnv/out100m1_hg19.gem
chrLenFile /work/gad/shared/pipeline/hg19/index/hg19.len
chrFiles /work/gad/shared/pipeline/hg19/index/chr/
lumpybase /work/gad/shared/bin/lumpy/lumpy-sv-master/
mapabilitybedgraph /work/gad/shared/pipeline/hg19/cnv/wgEncodeCrgMapabilityAlign100mer_no_uniq.bedgraph
blacklistfile /work/gad/shared/pipeline/hg19/cnv/wgEncodeDacMapabilityConsensusExcludable.txt
repeatmasker /work/gad/shared/pipeline/hg19/cnv/UCSC_rmsk.hg19.sort.bed.gz
bedtools /work/gad/shared/bin/bedtools
nist_bed /work/gad/shared/pipeline/hg19/nist/agilent_CRE.refseq_cds.NA12878_GIAB_highconf.intersect.hg19.bed
nist_vcf /work/gad/shared/pipeline/hg19/nist/NA12878_GIAB_highconf.agilent.refseq.intersect.vcf
hg19gtf /work/gad/shared/pipeline/hg19/refseq/hg19.refseq.with_genes.gtf
star2 /work/gad/shared/bin/STAR-2.5.2b/source
circosconfdir /work/gad/shared/pipeline/hg19/circos/
circosbin /work/gad/shared/bin/circos-0.69-2/bin/circos
rscript /soft/R/3.2.3/intel/13.1.3/bin/Rscript
snpeffbase /work/gad/shared/bin/snpEff
exacvcf /work/gad/shared/pipeline/hg19/ExAC/ExAC.r0.3.1.sites.vep.vcf.gz
exacscores /work/gad/shared/pipeline/hg19/ExAC/fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
dbnsfp /work/gad/shared/bin/snpEff/data/dbNSFP/dbNSFP2.9.txt.gz
gnomadex /work/gad/shared/pipeline/hg19/ExAC/gnomad.exomes.r2.0.2.sites.vcf.gz
gnomadge /work/gad/shared/pipeline/hg19/ExAC/gnomad.genomes.r2.0.2.sites.vcf.gz
gnomadchr /work/gad/shared/pipeline/hg19/ExAC/gnomad.genomes.r2.0.2.sites
hgmd_vcf /work/gad/shared/pipeline/hg19/HGMD/HGMD_PRO_2017.2_hg19.vcf
regulatoryfeatures /work/gad/shared/pipeline/hg19/ensembl_regulation/regulatory_features.bed
motiffeatures /work/gad/shared/pipeline/hg19/ensembl_regulation/motif_features.bed
encodednase /work/gad/shared/pipeline/hg19/Encode/wgEncodeRegDnaseClusteredV3.bed
encodetfbs /work/gad/shared/pipeline/hg19/Encode/wgEncodeRegTfbsClusteredV3.bed
linsight /work/gad/shared/pipeline/hg19/LINSIGHT
fantom /work/gad/shared/pipeline/hg19/FANTOM/fantom_cage_peak.bed
isgenic /work/gad/shared/pipeline/hg19/FANTOM/isGenic.bed
genelists /work/gad/shared/pipeline/hg19/gene_lists/
vtbase /work/gad/shared/bin/vt
annotate_variants_pharmAnnot.sh 0 → 100644
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#!/bin/ksh
### GAD PIPELINE ###
## annotate_variants_snpeff.sh
## Version : 1.0
## Description : This script allows user to launch SnpEff and SNpSift for basic variant annotation, frequency annotation and score annotation
## Usage : qsub -pe smp <nb thread> -v INPUTFILE=<raw/vcf/file>,OUTPUTFILE=</path/to/the/output/vcf/file>,PHARMGKB=<ref/file/pharmgkb>,[NOCHECK=yes|no],[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] annotate_variants_pharmAnnot.sh
## Output : .vcf file containing annotations
## Requirements : jdk 1.8.0
## Author : Simon.Verdez@u-bourgogne.fr
## Creation Date : 20180727
## last revision date : 20180727
## Known bugs : None
#$ -q batch
#$ -V
# Log file path option
if [ -z ${LOGFILE} ]
then
LOGFILE=annotate_variants_snpeff.$(date +"%F_%H-%M-%S").log
fi
# Config file path option
if [ -z ${CONFIGFILE} ]
then
CONFIGFILE=analysis_config.tsv
fi
# Logging
exec 1>> $LOGFILE 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if config file exist
if [ ! -f $CONFIGFILE ]
then
echo "Config file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
# Check if input file exist
if [ ! -f $INPUTFILE ]
then
echo "Input file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
if [ ! -f $PHARMGKB ]
then
echo "ref pharmgkb file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
# Check if output file is specified
if [ -z $OUTPUTFILE ]
then
echo "Output file is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}')
SNPEFF=$(grep "snpeffbase" $CONFIGFILE | awk '{print $2}')
# Launch Snpeff and SnpSift command and check exit code
echo "Command: $JAVA -Xmx4g -jar $SNPEFF/SnpSift.jar Annotate $PHARMGKB $INPUTFILE > $OUTPUTFILE"
bash -o pipefail -c "$JAVA -Xmx4g -jar $SNPEFF/SnpSift.jar Annotate $PHARMGKB $INPUTFILE > $OUTPUTFILE"
snpeff_exitcode=$?
echo "snpeff exit code : $snpeff_exitcode"
if [ $snpeff_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_Annot.failed
exit 1
fi
if [ -z ${NOCHECK} ] || [ ${NOCHECK} == "no" ]
then
chr=`tail -1 $OUTPUTFILE | cut -f1`
if [ $chr != "chrX" ] && [ $chr != "chrY" ] && [ $chr != "X" ] && [ $chr != "Y" ]
then
echo "vcf file does not seem complete"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
fi
echo "$(date +"%F_%H-%M-%S"): END"
create_html_v2.py
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haplo_scan.sh 0 → 100755
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#!/bin/bash
###GAD PIPELINE ###
## haplo_scan.sh
## Version : 1.0.0
## Description : This scprit tke a bam and return a file text with HLA type
## Usage : qsub -v BAM=<path to the bam>,SORTIE=<path to outdir>,GeneList=<path to gene list>,[LOGFILE=/path/to/the/log/file] haplo_scan.sh
## Output : file text
## Requirements : HLAscan
## Author : Simon.Verdez@etu.u-bourgogne.fr
## Creation Date : 20180425
## last revision date : 20180425
## Known bugs : None
#$ -N hlascan
#$ -q batch
#$ -pe smp 1
#$ -V
# Log file path option
if [ -z ${LOGFILE} ]
then
LOGFILE=haplo_scan.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> $LOGFILE 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exist
if [ ! -f $BAM ]
then
echo "Bam file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch haplo_scan.failed
exit 1
fi
# Check if gene file exist
if [ ! -f $GeneList ]
then
echo "Gene file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch haplo_scan.failed
exit 1
fi
# Check if config file exist
if [ ! -f $CONFIGFILE ]
then
echo "Config file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch annotate_variants_snpeff.failed
exit 1
fi
# Check if output file is specified
if [ -z $SORTIE ]
then
echo "SORTIE file is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch haplo_scan.failed
exit 1
fi
SAMPLE=`basename ${BAM} | cut -d . -f1`
RES=${SORTIE}
GL=/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
#Launch haplo_scan
/work/gad/shared/bin/miniconda2/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py $BAM $GL $RES
hla_exitcode=$?
echo "hla_scan exit code : $hla_exitcode"
if [ $hla_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch hla_scan.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
merge_GATK.sh 0 → 100644
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#!/bin/ksh
### PharmAnnot PIPELINE ###
## merge_GATK.sh
## Version : 1.0.0
## Description : This script merge two vcf file
## Usage : qsub -pe smp <nb thread> -v INPUTFILE1=</path/to/the/input/vcf/file>,INPUTFILE2=</path/to/the/input/vcf/file>,REF=</path/to/the/ref/file>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] merge_GATK.sh
## Output : .vcf file containing annotations
## Requirements : jdk 1.8.0
## Author : simon.verdez@chu-dijon.fr
## Creation Date : 20180702
## last revision date : 20180702
## Known bugs : None
#$ -q batch
#$ -V
# Log file path option
if [ -z ${LOGFILE} ]
then
LOGFILE=merge_GATK.$(date +"%F_%H-%M-%S").log
fi
# Config file path option
if [ -z ${CONFIGFILE} ]
then
CONFIGFILE=analysis_config.tsv
fi
# Logging
exec 1>> $LOGFILE 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if config file exist
if [ ! -f $CONFIGFILE ]
then
echo "Config file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch merge_GATK.failed
exit 1
fi
# Check if input1 file exist
if [ ! -f $INPUTFILE1 ]
then
echo "Input1 file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch merge_GATK.failed
exit 1
fi
# Check if input2 file exist
if [ ! -f $INPUTFILE2 ]
then
echo "Input2 file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch merge_GATK.failed
exit 1
fi
# Check if ref file exist
if [ ! -f $REF ]
then
echo "ref file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch merge_GATK.failed
exit 1
fi
# Check if output file is specified
if [ -z $OUTPUTFILE ]
then
echo "Output file is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch merge_GATK.failed
exit 1
fi
JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
PATHSCRIPT=$(grep "pipelinebase" $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"
$JAVA -jar $GATK -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE
genotypeMerge_exitcode=$?
echo "GenotypeMerge exit code : $genotypeMerge_exitcode"
if [ $genotypeMerge_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch merge.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
pharmconfig.tsv 0 → 100644
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HLAlist /work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
tsv2vcf.py
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#!/usr/bin/python
### PharmAnnot PIPELINE ###
## tsv2vcf.py
## Version : 1.1.0
## Description : Conversion a tsv file in vcf file.
## Usage : python tsv2vcf.py -i <input/tsv/file> -p <input/tsv/file> -m<input/tsv/file> -o <output/vcf/file> -e <log/file>
## Output : vcf file
## Requirements : python 2.7+
## Author : Simon.Verdez@chu-dijon.fr
## Creation Date : 20180709
## last revision date : 20180731
## Known bugs : None
import os
import sys
import vcf
import csv
from pyexcel_ods import *
from VCF_tools import *
import subprocess
from operator import *
import getopt
import logging
#Options
try:
opts, args = getopt.getopt(sys.argv[1:], 'i:p:m:o:e:')
for opt, arg in opts:
if opt in ("-i"):
tsvfile = arg
if opt in ("-p"):
pharmgkb = arg
if opt in ("-m"):
OMIM = arg
elif opt in ("-o"):
out_vcf = arg
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('tsvfile'):
logging.exception('No input file given')
sys.exit(1)
if not vars().has_key('pharmgkb'):
logging.exception('No pharmgkb database given')
sys.exit(1)
if not vars().has_key('OMIM'):
logging.exception('No OMIM database given')
sys.exit(1)
# Check files
try:
f = open(tsvfile, 'r')
f.close()
except IOError:
logging.exception('Input file does not exist')
sys.exit(1)
try:
f = open(pharmgkb, 'r')
f.close()
except IOError:
logging.exception('Clinvar file does not exist')
sys.exit(1)
try:
f = open(OMIM, 'r')
f.close()
except IOError:
logging.exception('Hgmd file does not exist')
sys.exit(1)
"""extraction du tableau """
data = get_data("/work/gad/sv347413/epilepsie/Pipeline/tableau pharmgkb.ods")
data2 = get_data("/work/gad/sv347413/epilepsie/Pipeline/tableau OMIM.ods")
"""Liste contenant les genes d'interets"""
ListeG = []
"""recuperation des genes dans le fichier"""
for i in range(len(data["hg19"])-1):
if not data["hg19"][i]:
pass
else:
if data["hg19"][i][1] != "gene":
"""remplissage de la liste"""
if data["hg19"][i][1] not in ListeG:
ListeG.append((data["hg19"][i][1]))
for i in range(len(data2["hg19"])-1):
if not data2["hg19"][i]:
pass
else:
if data2["hg19"][i][1] != "GENE":
if data2["hg19"][i][1] not in ListeG:
ListeG.append((data2["hg19"][i][1]))
#print(ListeG)
with open(pharmgkb) as pharmfile:
reader = csv.DictReader(pharmfile, dialect='excel-tab')
for row in reader:
if row['gene'] != "":
if row['gene'] not in ListeG:
ListeG.append(row['gene'])
with open(OMIM) as OMIMfile:
reader = csv.DictReader(OMIMfile, dialect='excel-tab')
for row in reader:
if row['GENE'] != "":
if row['GENE'] not in ListeG:
ListeG.append(row['GENE'])
#print ListeG
"""ecriture des lignes CNV dans le vcf"""
ListeVCF=[]
for gene in ListeG:
with open(sys.argv[1]) as tsvfile:
reader = csv.DictReader(tsvfile, dialect='excel-tab')
with open(tsvfile) as file:
reader = csv.DictReader(file, dialect='excel-tab')
for row in reader:
if gene in row['GeneList'] and gene != "":
line_vcf = VCF_CNV()
line_vcf.CHROM = row["#CHR"]
line_vcf.POS = row["START"]
p = subprocess.Popen(["samtools", 'faidx',"index/hg19_essential.fa", row["#CHR"]+":"+row["START"]+"-"+row["START"]], stdout = subprocess.PIPE)
p = subprocess.Popen(["samtools", 'faidx',"/work/gad/sv347413/epilepsie/Pipeline/index/hg19_essential.fa", row["#CHR"]+":"+row["START"]+"-"+row["START"]], stdout = subprocess.PIPE)
line_vcf.REF = p.stdout.readlines()[1].strip("\n")
line_vcf.ALT = "<"+row["CNV"]+">"
line_vcf.QUAL = "6"
......@@ -61,12 +123,6 @@ for gene in ListeG:
ListeVCF = sorted(ListeVCF,key=attrgetter('POS'))
#print ListeVCF
for line in ListeVCF:
with open (sys.argv[2],'a') as vcf_out:
with open (out_vcf,'a') as vcf_out:
vcf_out.write(repr(line)+"\n")
#test = vcf.Reader(filename = "header_CNV.vcf")
#for record in test:
# print record
wrapper_create_html.sh 0 → 100644
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#!/bin/ksh
### GAD PIPELINE ###
## wrapper_create_html.sh
## Version : 1.0.0
## Description : a wrapper for qsubing create_html.py script
## Usage : qsub -pe smp <nb thread> -v VCF_SNP=</path/to/the/input/vcf/file>,VCF_CNV=</path/to/the/input/vcf/file>,REPORTFILE=<path/to/the/HLAscan/report>,BAMFILE=</path/to/the/bam>,TSVFILE=</path/to/the/tsv>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_create_html.sh
## Output : create_html.py output
## Requirements : Recquire script create_html.py and VcfTools
## Author : Simon.Verdez@u-bourgogne.fr
## Creation Date : 20180802
## last revision date : 20180802
## Known bugs : None
#$ -q batch
#$ -V
# Log file path option
if [ -z ${LOGFILE} ]
then
LOGFILE=annotate_variants.$(date +"%F_%H-%M-%S").log
fi
# Config file path option
if [ -z ${CONFIGFILE} ]
then
CONFIGFILE=analysis_config.tsv
fi
# Logging
exec 1>> $LOGFILE 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if config file exist
if [ ! -f $VCF_SNP ]
then
echo "Vcf SNP file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
if [ ! -f $VCF_CNV ]
then
echo "Vcf CNV file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
if [ ! -f $REPORTFILE ]
then
echo "Report HLAscan file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
if [ ! -f $BAMFILE ]
then
echo "BAM file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
if [ ! -f $TSVFILE ]
then
echo "TSV file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
# Check if output file is specified
if [ -z $OUTPUTFILE ]
then
echo "Output file is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
PYTHONBIN=`grep pythonbin $CONFIGFILE | cut -f2`
PIPELINEBASE=`grep pipelinebase $CONFIGFILE | cut -f2`
# Launch python script command and check exit code
echo "command : $PIPELINEBASE/create_html.py -v $VCF_SNP -c $VCF_CNV -h $REPORTFILE -b $BAMFILE -t $TSVFILE -o $OUTPUTFILE -e $LOGFILE"
$PYTHONBIN $PIPELINEBASE/create_html.py -v $VCF_SNP -c $VCF_CNV -h $REPORTFILE -b $BAMFILE -t $TSVFILE -o $OUTPUTFILE -e $LOGFILE
create_html_exitcode=$?
echo "create_html exit code : $annotate_variants_exitcode"
if [ $creaete_html_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch create_html.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
wrapper_tsv2vcf.sh 0 → 100644
View file @ 5f8e477e
#!/bin/ksh
### GAD PIPELINE ###
## wrapper_tsv2vcf.sh
## Version : 1.0.0
## Description : a wrapper for qsubing tsv2vcf.py script
## Usage : qsub -pe smp <nb thread> -v INPUTFILE=</path/to/the/input/tsv/file>,PHARMGKB=<ref/file/pharmgkb>,OMIM=<ref/file/OMIM>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_tsv2vcf.sh
## Output : annotate_variants.py output
## Requirements : Recquire script tsv2vcf.py and VcfTools
## Author : Simon.Verdez@u-bourgogne.fr
## Creation Date : 20180702
## last revision date : 20180702
## Known bugs : None
#$ -q batch
#$ -V
Log file path option
if [ -z ${LOGFILE} ]
then
LOGFILE=annotate_variants.$(date +"%F_%H-%M-%S").log
fi
# Config file path option
if [ -z ${CONFIGFILE} ]
then
CONFIGFILE=analysis_config.tsv
fi
# Logging
exec 1>> $LOGFILE 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if config file exist
if [ ! -f $CONFIGFILE ]
then
echo "Config file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
# Check if input file exist
if [ ! -f $INPUTFILE ]
then
echo "Input file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
if [ ! -f $PHARMGKB ]
then
echo "PHARMGKB reference file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
if [ ! -f $OMIM ]
then
echo "OMIM reference file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
# Check if output file is specified
if [ -z $OUTPUTFILE ]
then
echo "Output file is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
PYTHONBIN=`grep pythonbin $CONFIGFILE | cut -f2`
PIPELINEBASE=`grep pipelinebase $CONFIGFILE | cut -f2`
# Launch python script command and check exit code
echo "command : $PIPELINEBASE/tsv2vcf.py -i $INPUTFILE -p $PHARMGKB -m $OMIM -o $OUTPUTFILE -e $LOGFILE"
$PYTHONBIN $PIPELINEBASE/tsv2vcf.py -i $INPUTFILE -p $PHARMGKB -m $OMIM -o $OUTPUTFILE -e $LOGFILE
tsv2vcf_exitcode=$?
echo "tsv2vcf exit code : $tsv2vcf_exitcode"
if [ $tsv2vcf_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch tsv2vcf.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
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