def extract_file(path, destination, flags=''):
print ' Extracting file: ' + path + ' into: ' + destination
mkdir(destination)
command = 'tar xf ' + path + ' -C ' + destination + ' ' + flags
run_command(command, Exception)
ok(' ok\n')
return True
def exists(path):
print ' Checking for existence of: ' + path
if os.path.isfile(path):
ok('Already here: \n ' + path)
return True
warning('Not here!')
return False
def prepare_input_files(args=None):
mkdir(args.download)
mkdir(args.hg)
if not exists(os.path.join(args.download, 'chromFa.tar.gz')):
if not download_file(args.hg, downloadURLs['hg19'], args.download):
raise Exception('Something went wrong while downloading the reference file')
if not extract_file(joiner(args.download, 'chromFa.tar.gz'), joiner(args.hg, 'chromFa')):
raise Exception('Something went wrong while extracting the reference file.')
if not download_file('dbsnp_138.hg19.vcf.gz', downloadURLs['dbsnp'], joiner(args.hg, 'chromFa')):
raise Exception('Something went wrong while downloading the reference file')
with cwd(joiner(args.hg, 'chromFa')):
command = 'cat chrM.fa chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa\
chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa\
chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.fa > hg19.fa'
run_command(command, Exception)
# command = 'wget ftp://[email protected]/bundle/2.8/hg19/dbsnp_138.hg19.vcf.gz 2>/dev/null'
# run_command(command, Exception)
command = 'gunzip -f dbsnp_138.hg19.vcf.gz'
run_command(command, Exception)
command = 'module add ' + ngs_tools_dict['bwa'] + ' && bwa index -a bwtsw -p hg19 hg19.fa'
run_command(command, Exception)
command = 'module add ' + ngs_tools_dict['SamTools'] + ' && samtools faidx hg19.fa'
run_command(command, Exception)
command = 'module add ' + ngs_tools_dict['Picard'] + ' && $PICARDRUN CreateSequenceDictionary REFERENCE=hg19.fa OUTPUT=hg19.dict'
run_command(command, Exception)
ok(' ok\n')
return True