def pseudoalign(fqs,
sample,
paired,
reference,
outdir,
temp,
threads,
keep_files,
partial=False):
'''Calls Kallisto to pseudoalign reads.'''
file_list = []
# Get read length stats
reads_file = ''.join([temp, sample, '.reads.txt'])
num, avg, std = analyze_reads(fqs, paired, reads_file, keep_files)
# Kallisto fails if std used for single-end is 0
if std == 0: std = .00001
temp2 = check_path(''.join([temp, sample]))
command = ['kallisto pseudo -i', reference, '-t', threads, '-o', temp2]
if paired:
command.extend([fqs[0], fqs[1]])
else:
fq = fqs[0]
command.extend(['--single -l', str(avg), '-s', str(std), fq])
run_command(command, '[alignment] Pseudoaligning with Kallisto: ')
# Move and rename Kallisto output
file_in = ''.join([temp2, 'pseudoalignments.tsv'])
count_file = ''.join([temp, sample, '.counts.tsv'])
file_list.append(file_in)
run_command(['mv', file_in, count_file])
file_in = ''.join([temp2, 'pseudoalignments.ec'])
eq_file = ''.join([temp, sample, '.eq.tsv'])
file_list.append(file_in)
run_command(['mv', file_in, eq_file])
run_command(['rm -rf', temp2])
remove_files(file_list, keep_files)
return count_file, eq_file, num, avg, std
help='keep intermediate files\n\n',
default=False)
parser.add_argument('-t',
'--threads',
type = str,
default='1')
parser.add_argument('-v',
'--verbose',
action = 'count',
default=False)
args = parser.parse_args()
temp, outdir = [check_path(path) for path in [args.temp,args.outdir]]
sample = os.path.basename(args.bam).split('.')[0]
if args.log:
log_file = args.log
else:
log_file = ''.join([outdir,sample,'.extract.log'])
with open(log_file, 'w'):
pass
if args.verbose:
handlers = [log.FileHandler(log_file), log.StreamHandler()]
log.basicConfig(level=log.DEBUG,
type=str,
help='run name\n\n',
default='',
metavar='')
parser.add_argument('-v',
'--verbose',
action = 'count',
default=False)
args = parser.parse_args()
if args.run: args.run += '.'
indir, outdir = [check_path(path) for path in [args.indir, args.outdir]]
(genotype_files, partial_files,
gene_count_files, quant_files) = get_paths(indir)
if genotype_files:
process_json(genotype_files, indir, outdir,
args.run, 'genotypes')
if partial_files:
process_json(partial_files, indir, outdir,
args.run, 'partial_genotypes')
if gene_count_files:
process_json(gene_count_files, indir, outdir,
args.run, 'genes')
'--verbose',
action = 'count',
default=False)
args = parser.parse_args()
if args.verbose:
log.basicConfig(level = log.DEBUG, format = '%(message)s')
else:
handlers = [log.StreamHandler()]
log.basicConfig(format = '%(message)s')
log.info('')
hline()
check_path('dat/ref')
if args.update:
log.info('[reference] Updating HLA reference')
checkout_version('origin')
build_fasta()
elif args.rebuild:
build_fasta()
elif args.version:
if args.version not in versions:
sys.exit('[reference] Error: invalid version.')
checkout_version(versions[args.version])
build_fasta()
metavar = '')
parser.add_argument('--output_nomenclature',
type = str,
help = 'input nomenclature (current, polysolver)',
default = 'current',
metavar = '')
parser.add_argument('-v',
'--verbose',
action = 'count',
default=False)
args = parser.parse_args()
outdir = check_path(args.outdir)
if os.path.isdir(args.input):
# add convert polysolver output
indir = check_path(args.input)
genotype_files, partial_files, count_files, quant_files = get_paths(indir)
if genotype_files:
process_json(genotype_files,
indir,
outdir,
args.run,
'genotypes.json')
)
parser.add_argument('-v', '--verbose', action='count', default=False)
args = parser.parse_args()
if args.verbose:
log.basicConfig(level=log.DEBUG, format='%(message)s')
else:
handlers = [log.StreamHandler()]
log.basicConfig(format='%(message)s')
log.info('')
hline()
check_path(rootDir + 'dat/ref')
if args.update:
log.info('[reference] Updating HLA reference')
checkout_version('origin')
build_fasta()
elif args.rebuild:
build_fasta()
elif args.version:
if args.version not in versions:
sys.exit('[reference] Error: invalid version.')
checkout_version(versions[args.version])
build_fasta()
parser.add_argument('--keep_files',
action='count',
help='keep intermediate files\n\n',
default=False)
parser.add_argument('-t', '--threads', type=str, default='1', metavar='')
parser.add_argument('-v', '--verbose', action='count', default=False)
args = parser.parse_args()
if len(args.file) == 0:
sys.exit('[genotype] Error: FASTQ or alignment.p file required')
sample = os.path.basename(args.file[0]).split('.')[0]
temp, outdir = [check_path(path) for path in [args.temp, args.outdir]]
if args.log:
log_file = args.log
else:
log_file = ''.join([outdir, sample, '.genotype.log'])
with open(log_file, 'w'):
pass
if args.verbose:
handlers = [log.FileHandler(log_file), log.StreamHandler()]
log.basicConfig(level=log.DEBUG,
format='%(message)s',
handlers=handlers)
