def parse_args(args):
"""Parse the command line arguments.
"""
# Convert ~ to real path, and get input files
if args['<in2.fastq>']:
fin1 = os.path.expanduser(args['<in1.fastq>'])
fin2 = os.path.expanduser(args['<in2.fastq>'])
input_files = [fin1, fin2]
else:
fin = os.path.expanduser(args['<input.fastq>'])
input_files = [fin]
num_threads = int(args['--threads'])
compress = args['--compress']
outdir = args_to_out_dir(args)
phred = args['--phred']
if phred not in ('33', '64'):
raise CannotContinueException(
"""Phred score {} is not supported.""".format(phred))
phred = int(phred)
trimmomatic_args = args['--trimmomatic'].strip("'").strip('"').strip("'")
return (num_threads, outdir, compress, phred, trimmomatic_args,
input_files)
def parse_args(args):
"""Parse the command line arguments."""
debug_switch = args['--debug-switch']
dump_rg_db = args['--debug-dump-rg-db']
dump_loc_db = args['--debug-dump-loc-db']
# Convert ~ to real path
input_file = os.path.expanduser(args['<alignment-file>'])
# Which kit?
kit = args['--kit']
if kit == KIT_BIOO:
pass
else:
raise CannotContinueException(
"""Kit {} is not supported.""".format(kit))
# Figure out which function to use to write to output file.
num_threads = args['--threads']
# Which store to use
if args['--store'] not in (STORE_OPTION_LMDB, STORE_OPTION_MEMORY):
raise CannotContinueException("""Store {} is not supported.""".format(
args['--store']))
store = args['--store']
outdir = args_to_out_dir(args)
return (kit, store, outdir, input_file, debug_switch, dump_rg_db,
dump_loc_db)
def parse_args(args):
"""Parse the command line arguments."""
# Convert ~ to real path (strip silly leading './' too)
if args['<in2.fastq>']:
# PE mode
in1 = os.path.expanduser(args['<in1.fastq>'])
in2 = os.path.expanduser(args['<in2.fastq>'])
input_files = (in1, in2)
else:
fin = os.path.expanduser(args['<input.fastq>'])
input_files = (fin, )
# Figure out which function to use to write to output file.
compress = args['--compress']
num_threads = int(args['--threads'])
if num_threads > 1 and which('pigz') and compress:
# return a partial for pigzwrite
write_func = functools.partial(pigzwrite, num_threads)
else:
write_func = functools.partial(open, mode='w')
outdir = args_to_out_dir(args)
# optional trimlog
opt_trimlog = args['-l'] if args['-l'] else None
return (write_func, outdir, compress, opt_trimlog, input_files)
def parse_args(args):
"""Parse the command line arguments."""
debug_switch = args['--debug-switch']
dump_rg_db = args['--dump-rg-db']
dump_loc_db = args['--dump-loc-db']
dump_dup_group_db = args['--dump-dup-group-db']
dump_dup_db = args['--dump-dup-db']
dump_umi_error_db = args['--dump-umi-error-db']
random_seed = args['--random-seed']
write_dedupped_sam = not args['--no-write-dedupped-sam']
write_flagged_sam = args['--write-flagged-sam']
write_dup_only_sam = not args['--no-write-dup-sam']
write_dup_group_sam_like = not args['--no-write-dup-group-file']
write_sam_headers = not args['--no-write-sam-headers']
paired = False if args['--unpaired'] else True
reject_umi_errors = not args['--keep-bad-umis']
correct_umis = args['--correct-umis']
build_read_and_loc_dbs = not args['--debug-no-build-read-and-loc-dbs']
# Convert ~ to real path
input_file = os.path.expanduser(args['<alignment-file>'])
# Which kit?
kit = str(args['--kit']).lower()
if kit == KIT_BIOO:
write_umi_error_rejects = True
else:
write_umi_error_rejects = False
if correct_umis and kit != KIT_BIOO:
raise CannotContinueException(
"""Cannot correct UMIs when kit is not Bioo.""")
if reject_umi_errors and correct_umis:
raise CannotContinueException(
"Doesn't make sense to reject and *also* correct erroneous UMIs!!"
" If passing --correct, you must also pass --keep-bad-umis.")
# Which store to use
if args['--store'] == None:
store = STORE_OPTION_MEMORY
elif args['--store'] not in (STORE_OPTION_LMDB, STORE_OPTION_MEMORY):
raise CannotContinueException("""Store {} is not supported.""".format(
args['--store']))
else:
store = args['--store']
outdir = args_to_out_dir(args)
return (kit, store, outdir, input_file, paired, build_read_and_loc_dbs,
reject_umi_errors, correct_umis, write_dedupped_sam,
write_flagged_sam, write_dup_only_sam, write_dup_group_sam_like,
write_umi_error_rejects, write_sam_headers, random_seed,
debug_switch, dump_rg_db, dump_loc_db, dump_dup_group_db,
dump_dup_db, dump_umi_error_db)
def parse_args(args):
"""Parse the command line arguments. """
umi_reads_file = os.path.expanduser(args['<in.umi.fq>'])
barcode_reads_file = os.path.expanduser(args['<in.barcode.fq>'])
barcode_list_file = os.path.expanduser(args['<barcode_file>'])
delete_temp_files_upon_failure = not args['--no-delete-tmp-files']
write_rejects_files = not args['--no-write-rejects']
min_umi_qual = int(args['--umi-min-qual'])
umi_qf_win_size = int(args['--umi-qf-win-size'])
# phred
if args['--phred'] not in ('33', '64'):
raise ArgumentException("ERR212: --phred can be only '33' or '64'.")
phred = int(args['--phred'])
# Paired or single end?
if args['<in.R2.fq>']:
# mode = PE
paired = True
# Convert ~ to real path
args['<in.R1.fq>'] = os.path.expanduser(args['<in.R1.fq>'])
args['<in.R2.fq>'] = os.path.expanduser(args['<in.R2.fq>'])
reads_files = [args['<in.R1.fq>'], args['<in.R2.fq>']]
else:
# Convert ~ to real path
args['<in.fq>'] = os.path.expanduser(args['<in.fq>'])
# mode = SR
paired = False
reads_files = [args['<in.fq>']]
fp_write = functools.partial(open, mode='w')
# Return an appropriate function pointer for annotation.
if paired:
fp_split_qf_umi_anno_raw = split_qf_umi_anno_raw_pe
else:
fp_split_qf_umi_anno_raw = split_qf_umi_anno_raw_sr
outdir = args_to_out_dir(args)
return (fp_split_qf_umi_anno_raw, fp_write, outdir, phred, min_umi_qual,
umi_qf_win_size, write_rejects_files,
delete_temp_files_upon_failure, barcode_list_file,
barcode_reads_file, umi_reads_file, reads_files)
def parse_args(args):
"""Parse the command line arguments."""
adapters = []
# Convert ~ to real path
if args['<in2.fastq>']:
in1 = os.path.expanduser(args['<in1.fastq>'])
in2 = os.path.expanduser(args['<in2.fastq>'])
input_files = [in1, in2]
if not args['--adapter1'] or not args['--adapter2']:
raise ArgumentException("""Error:
--adapter1 and --adapter2 are required if running in
paired-end mode (i.e. when you give two FASTQ files).
""")
adapters = [args['--adapter1'], args['--adapter2']]
else:
input_files = [os.path.expanduser(args['<input.fastq>'])]
adapters = [args['--adapter1']]
# Uncomment if we ever remove the default from the --apapter arguments
# if args['--adapter2']:
# raise ArgumentException(
# """Error:
# --adapter2 was given (suggesting you wanted paired-end
# adapter removal), but only one FASTQ file was given.
# """)
outdir = args_to_out_dir(args)
cutadapt_args = args['--cutadapt'].strip("'").strip('"').strip("'")
# compress output?
compress = args['--compress']
return (compress, outdir, cutadapt_args, adapters, input_files)
def parse_args(args):
"""Parse the command line arguments. """
# Paired or single end? FASTQ or BAM?
if args['<in2.fastq>']:
# mode = FASTQ, PE
paired = True
filetype = 'FASTQ'
# Convert ~ to real path
args['<in1.fastq>'] = os.path.expanduser(args['<in1.fastq>'])
args['<in2.fastq>'] = os.path.expanduser(args['<in2.fastq>'])
input_files = [args['<in1.fastq>'], args['<in2.fastq>']]
else:
# Convert ~ to real path
args['<input.fastq>'] = os.path.expanduser(args['<input.fastq>'])
# Note: If you write the following for docopt:
# dupliganger remove-umi [options] <input.fastq>
# dupliganger remove-umi [options] <input.bam>
# then it will always populate <input.fastq> and never populate
# <input.bam>, hence the somewhat confusing names going on down
# below...
if is_bam(args['<input.fastq>']):
# It is a bam, so hack docopt a bit
args['<input.bam>'] = args['<input.fastq>']
args['<input.fastq>'] = None
paired = True if is_paired_bam(args['<input.bam>']) else False
filetype = 'BAM'
input_files = [args['<input.bam>']]
else:
# mode = FASTQ, SR
paired = False
filetype = 'FASTQ'
input_files = [args['<input.fastq>']]
# What fp_extract_umi to use?
kit = args['--kit']
if kit == KIT_BIOO:
if paired:
fp_extract_umi = extract_paired_umis_bioo
else:
fp_extract_umi = extract_single_umi_bioo
else:
raise CannotContinueException(
"""Kit {} is not supported.""".format(kit))
# Figure out which function to use to write to output file.
num_threads = int(args['--threads'])
compress = args['--compress']
if num_threads > 1 and which('pigz') and compress:
# return a partial for pigzwrite
# TODO: Maybe alter this to num_threads/2 if --paired-end?
fp_write = functools.partial(pigzwrite, num_threads)
elif which('gzip') and compress:
# return a partial for gzwrite
fp_write = gzwrite
else:
fp_write = functools.partial(open, mode='w')
# Return an appropriate function pointer for annotation.
if filetype == 'FASTQ':
if paired:
fp_anno = create_annotated_files_from_fastq
else:
fp_anno = create_annotated_file_from_fastq
elif filetype == 'BAM':
if paired:
fp_anno = create_annotated_files_from_bam
else:
fp_anno = create_annotated_file_from_bam
else:
raise ControlFlowException("""ERR213: Not possible to be here.""")
outdir = args_to_out_dir(args)
if args['--force-paired'] and not paired:
sys.stderr.write(
"WARNING: Passed --force-paired but {} appears not to be "
"paired-end.\n")
force_paired = args['--force-paired']
return (fp_extract_umi, fp_anno, fp_write, outdir, compress, force_paired,
input_files)