def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
# declare temp arrays
temp_files = [] # files to deleted later at the end
# if bowtie2 index is tarball then unpack it
if args.bowtie2_index_prefix_or_tar.endswith('.tar') or \
args.bowtie2_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bowtie2 index tar...')
tar = args.bowtie2_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bowtie2_index_prefix = find_bowtie2_index_prefix(args.out_dir)
temp_files.append('{}*'.format(
bowtie2_index_prefix))
else:
bowtie2_index_prefix = args.bowtie2_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bowtie2_index(bowtie2_index_prefix)
# bowtie2
log.info('Running bowtie2...')
if args.paired_end:
bam, align_log = bowtie2_pe(
args.fastqs[0], args.fastqs[1],
bowtie2_index_prefix,
args.multimapping, args.nth,
args.out_dir)
else:
bam, align_log = bowtie2_se(
args.fastqs[0],
bowtie2_index_prefix,
args.multimapping, args.nth,
args.out_dir)
log.info('Removing temporary files...')
print(temp_files)
rm_f(temp_files)
log.info('Showing align log...')
run_shell_cmd('cat {}'.format(align_log))
log.info('Checking if BAM file is empty...')
if not int(run_shell_cmd('samtools view -c {}'.format(bam))):
raise ValueError('BAM file is empty, no reads found.')
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
# declare temp arrays
temp_files = [] # files to deleted later at the end
# if bwa index is tarball then unpack it
if args.bwa_index_prefix_or_tar.endswith('.tar') or \
args.bwa_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bwa index tar...')
tar = args.bwa_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bwa_index_prefix = find_bwa_index_prefix(args.out_dir)
temp_files.append('{}*'.format(
bwa_index_prefix))
else:
bwa_index_prefix = args.bwa_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bwa_index(bwa_index_prefix)
# bwa
log.info('Running bwa...')
if args.paired_end:
bam = bwa_pe(
args.fastqs[0], args.fastqs[1],
bwa_index_prefix, args.nth, args.mem_gb, args.use_bwa_mem_for_pe,
args.bwa_mem_read_len_limit, args.rescue_reads_for_bwa_mem,
args.out_dir)
else:
bam = bwa_se(
args.fastqs[0],
bwa_index_prefix, args.nth, args.mem_gb,
args.out_dir)
log.info('Removing temporary files...')
rm_f(temp_files)
log.info('Checking if BAM file is empty...')
if bam_is_empty(bam, args.nth):
raise ValueError('BAM file is empty, no reads found.')
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
def main():
# read params
args = parse_arguments()
log.info('Initializing and making output directory...')
mkdir_p(args.out_dir)
# declare temp arrays
temp_files = [] # files to deleted later at the end
# if bwa index is tarball then unpack it
if args.bwa_index_prefix_or_tar.endswith('.tar') or \
args.bwa_index_prefix_or_tar.endswith('.tar.gz'):
log.info('Unpacking bwa index tar...')
tar = args.bwa_index_prefix_or_tar
# untar
untar(tar, args.out_dir)
bwa_index_prefix = os.path.join(args.out_dir,
os.path.basename(strip_ext_tar(tar)))
temp_files.append('{}.*'.format(bwa_index_prefix))
else:
bwa_index_prefix = args.bwa_index_prefix_or_tar
# check if bowties indices are unpacked on out_dir
chk_bwa_index(bwa_index_prefix)
# bwa
log.info('Running bwa...')
if args.paired_end:
bam = bwa_pe(args.fastqs[0], args.fastqs[1], bwa_index_prefix,
args.nth, args.use_bwa_mem_for_pe, args.out_dir)
else:
bam = bwa_se(args.fastqs[0], bwa_index_prefix, args.nth, args.out_dir)
log.info('Removing temporary files...')
rm_f(temp_files)
log.info('Checking if BAM file is empty...')
if not int(run_shell_cmd('samtools view -c {}'.format(bam))):
raise ValueError('BAM file is empty, no reads found.')
log.info('List all files in output directory...')
ls_l(args.out_dir)
log.info('All done.')
