def open_output_files(options, default_outfile, interleaved):
"""
Return an OutputFiles instance. If demultiplex is True, the untrimmed, untrimmed2, out and out2
attributes are not opened files, but paths (out and out2 with the '{name}' template).
"""
rest_file = info_file = wildcard = None
if options.rest_file is not None:
rest_file = xopen(options.rest_file, 'w')
if options.info_file is not None:
info_file = xopen(options.info_file, 'w')
if options.wildcard_file is not None:
wildcard = xopen(options.wildcard_file, 'w')
def open2(path1, path2):
file1 = file2 = None
if path1 is not None:
file1 = xopen(path1, 'w')
if path2 is not None:
file2 = xopen(path2, 'w')
return file1, file2
too_short = too_short2 = None
if options.minimum_length is not None:
too_short, too_short2 = open2(options.too_short_output, options.too_short_paired_output)
too_long = too_long2 = None
if options.maximum_length is not None:
too_long, too_long2 = open2(options.too_long_output, options.too_long_paired_output)
if int(options.discard_trimmed) + int(options.discard_untrimmed) + int(
options.untrimmed_output is not None) > 1:
raise CommandLineError("Only one of the --discard-trimmed, --discard-untrimmed "
"and --untrimmed-output options can be used at the same time.")
demultiplex = options.output is not None and '{name}' in options.output
if options.paired_output is not None and (demultiplex != ('{name}' in options.paired_output)):
raise CommandLineError('When demultiplexing paired-end data, "{name}" must appear in '
'both output file names (-o and -p)')
if demultiplex:
if options.discard_trimmed:
raise CommandLineError("Do not use --discard-trimmed when demultiplexing.")
out = options.output
untrimmed = options.output.replace('{name}', 'unknown')
if options.untrimmed_output:
untrimmed = options.untrimmed_output
if options.discard_untrimmed:
untrimmed = None
if options.paired_output is not None:
out2 = options.paired_output
untrimmed2 = options.paired_output.replace('{name}', 'unknown')
if options.untrimmed_paired_output:
untrimmed2 = options.untrimmed_paired_output
if options.discard_untrimmed:
untrimmed2 = None
else:
untrimmed2 = out2 = None
else:
untrimmed, untrimmed2 = open2(options.untrimmed_output, options.untrimmed_paired_output)
out, out2 = open2(options.output, options.paired_output)
if out is None:
out = default_outfile
if demultiplex:
assert out is not None and '{name}' in out and (out2 is None or '{name}' in out2)
return OutputFiles(
rest=rest_file,
info=info_file,
wildcard=wildcard,
too_short=too_short,
too_short2=too_short2,
too_long=too_long,
too_long2=too_long2,
untrimmed=untrimmed,
untrimmed2=untrimmed2,
out=out,
out2=out2,
demultiplex=demultiplex,
interleaved=interleaved,
)
def open_output_files(args, default_outfile,
file_opener: FileOpener) -> OutputFiles:
"""
Return an OutputFiles instance. If demultiplex is True, the untrimmed, untrimmed2, out and out2
attributes are not opened files, but paths (out and out2 with the '{name}' template).
"""
rest_file = file_opener.xopen_or_none(args.rest_file, "wb")
info_file = file_opener.xopen_or_none(args.info_file, "wb")
wildcard = file_opener.xopen_or_none(args.wildcard_file, "wb")
too_short = too_short2 = None
if args.minimum_length is not None:
too_short, too_short2 = file_opener.xopen_pair(
args.too_short_output, args.too_short_paired_output, "wb")
too_long = too_long2 = None
if args.maximum_length is not None:
too_long, too_long2 = file_opener.xopen_pair(
args.too_long_output, args.too_long_paired_output, "wb")
if int(args.discard_trimmed) + int(args.discard_untrimmed) + int(
args.untrimmed_output is not None) > 1:
raise CommandLineError(
"Only one of the --discard-trimmed, --discard-untrimmed "
"and --untrimmed-output options can be used at the same time.")
demultiplex_mode = determine_demultiplex_mode(args)
if demultiplex_mode and args.discard_trimmed:
raise CommandLineError(
"Do not use --discard-trimmed when demultiplexing.")
if demultiplex_mode == "normal":
out = args.output
untrimmed = args.output.replace('{name}', 'unknown')
if args.untrimmed_output:
untrimmed = args.untrimmed_output
if args.discard_untrimmed:
untrimmed = None
if args.paired_output is not None:
out2 = args.paired_output
untrimmed2 = args.paired_output.replace('{name}', 'unknown')
if args.untrimmed_paired_output:
untrimmed2 = args.untrimmed_paired_output
if args.discard_untrimmed:
untrimmed2 = None
else:
untrimmed2 = out2 = None
assert out is not None and '{name}' in out and (out2 is None
or '{name}' in out2)
elif demultiplex_mode == "combinatorial":
out = args.output
out2 = args.paired_output
if args.untrimmed_output or args.untrimmed_paired_output:
raise CommandLineError(
"Combinatorial demultiplexing (with {name1} and {name2})"
" cannot be combined with --untrimmed-output or --untrimmed-paired-output"
)
if args.discard_untrimmed:
untrimmed = untrimmed2 = None
else:
untrimmed = untrimmed2 = 'unknown'
else:
untrimmed, untrimmed2 = file_opener.xopen_pair(
args.untrimmed_output, args.untrimmed_paired_output, "wb")
out, out2 = file_opener.xopen_pair(args.output, args.paired_output,
"wb")
if out is None:
out = default_outfile
return OutputFiles(
rest=rest_file,
info=info_file,
wildcard=wildcard,
too_short=too_short,
too_short2=too_short2,
too_long=too_long,
too_long2=too_long2,
untrimmed=untrimmed,
untrimmed2=untrimmed2,
out=out,
out2=out2,
demultiplex=bool(demultiplex_mode),
force_fasta=args.fasta,
)
def open_output_files(
args,
default_outfile,
file_opener: FileOpener,
adapter_names: Sequence[str],
adapter_names2: Sequence[str],
) -> OutputFiles:
"""
Return an OutputFiles instance. If demultiplex is True, the untrimmed, untrimmed2, out and out2
attributes are not opened files, but paths (out and out2 with the '{name}' template).
"""
rest_file = file_opener.xopen_or_none(args.rest_file, "wb")
info_file = file_opener.xopen_or_none(args.info_file, "wb")
wildcard = file_opener.xopen_or_none(args.wildcard_file, "wb")
too_short = too_short2 = None
if args.minimum_length is not None:
too_short, too_short2 = file_opener.xopen_pair(
args.too_short_output, args.too_short_paired_output, "wb")
too_long = too_long2 = None
if args.maximum_length is not None:
too_long, too_long2 = file_opener.xopen_pair(
args.too_long_output, args.too_long_paired_output, "wb")
if int(args.discard_trimmed) + int(args.discard_untrimmed) + int(
args.untrimmed_output is not None) > 1:
raise CommandLineError(
"Only one of the --discard-trimmed, --discard-untrimmed "
"and --untrimmed-output options can be used at the same time.")
demultiplex_mode = determine_demultiplex_mode(args)
if demultiplex_mode and args.discard_trimmed:
raise CommandLineError(
"Do not use --discard-trimmed when demultiplexing.")
if demultiplex_mode == "normal":
out = out2 = None
combinatorial_out = combinatorial_out2 = None
demultiplex_out, demultiplex_out2, untrimmed, untrimmed2 = open_demultiplex_out(
adapter_names, args, file_opener)
elif demultiplex_mode == "combinatorial":
assert '{name1}' in args.output and '{name2}' in args.output
assert '{name1}' in args.paired_output and '{name2}' in args.paired_output
out = out2 = None
demultiplex_out = demultiplex_out2 = None
combinatorial_out, combinatorial_out2, untrimmed, untrimmed2 = open_combinatorial_out(
adapter_names, adapter_names2, args, file_opener)
else:
combinatorial_out = combinatorial_out2 = None
demultiplex_out = demultiplex_out2 = None
untrimmed, untrimmed2 = file_opener.xopen_pair(
args.untrimmed_output, args.untrimmed_paired_output, "wb")
out, out2 = file_opener.xopen_pair(args.output, args.paired_output,
"wb")
if out is None:
out = default_outfile
return OutputFiles(
rest=rest_file,
info=info_file,
wildcard=wildcard,
too_short=too_short,
too_short2=too_short2,
too_long=too_long,
too_long2=too_long2,
untrimmed=untrimmed,
untrimmed2=untrimmed2,
out=out,
out2=out2,
demultiplex_out=demultiplex_out,
demultiplex_out2=demultiplex_out2,
combinatorial_out=combinatorial_out,
combinatorial_out2=combinatorial_out2,
force_fasta=args.fasta,
)
def open_output_files(args, default_outfile, interleaved):
"""
Return an OutputFiles instance. If demultiplex is True, the untrimmed, untrimmed2, out and out2
attributes are not opened files, but paths (out and out2 with the '{name}' template).
"""
compression_level = args.compression_level
rest_file = info_file = wildcard = None
if args.rest_file is not None:
rest_file = xopen(args.rest_file, 'w', compresslevel=compression_level)
if args.info_file is not None:
info_file = xopen(args.info_file, 'w', compresslevel=compression_level)
if args.wildcard_file is not None:
wildcard = xopen(args.wildcard_file,
'w',
compresslevel=compression_level)
def open2(path1, path2):
file1 = file2 = None
if path1 is not None:
file1 = xopen(path1, 'wb', compresslevel=compression_level)
if path2 is not None:
file2 = xopen(path2, 'wb', compresslevel=compression_level)
return file1, file2
too_short = too_short2 = None
if args.minimum_length is not None:
too_short, too_short2 = open2(args.too_short_output,
args.too_short_paired_output)
too_long = too_long2 = None
if args.maximum_length is not None:
too_long, too_long2 = open2(args.too_long_output,
args.too_long_paired_output)
if int(args.discard_trimmed) + int(args.discard_untrimmed) + int(
args.untrimmed_output is not None) > 1:
raise CommandLineError(
"Only one of the --discard-trimmed, --discard-untrimmed "
"and --untrimmed-output options can be used at the same time.")
demultiplex = args.output is not None and '{name}' in args.output
if args.paired_output is not None and (demultiplex !=
('{name}' in args.paired_output)):
raise CommandLineError(
'When demultiplexing paired-end data, "{name}" must appear in '
'both output file names (-o and -p)')
demultiplex_combinatorial = (args.output is not None
and args.paired_output is not None
and '{name1}' in args.output
and '{name2}' in args.output
and '{name1}' in args.paired_output
and '{name2}' in args.paired_output)
if (demultiplex or demultiplex_combinatorial) and args.discard_trimmed:
raise CommandLineError(
"Do not use --discard-trimmed when demultiplexing.")
if demultiplex:
if demultiplex_combinatorial:
raise CommandLineError(
"You cannot combine {name} with {name1} and {name2}")
out = args.output
untrimmed = args.output.replace('{name}', 'unknown')
if args.untrimmed_output:
untrimmed = args.untrimmed_output
if args.discard_untrimmed:
untrimmed = None
if args.paired_output is not None:
out2 = args.paired_output
untrimmed2 = args.paired_output.replace('{name}', 'unknown')
if args.untrimmed_paired_output:
untrimmed2 = args.untrimmed_paired_output
if args.discard_untrimmed:
untrimmed2 = None
else:
untrimmed2 = out2 = None
assert out is not None and '{name}' in out and (out2 is None
or '{name}' in out2)
elif demultiplex_combinatorial:
out = args.output
out2 = args.paired_output
if args.untrimmed_output or args.untrimmed_paired_output:
raise CommandLineError(
"Combinatorial demultiplexing (with {name1} and {name2})"
" cannot be combined with --untrimmed-output or --untrimmed-paired-output"
)
if args.discard_untrimmed:
untrimmed = untrimmed2 = None
else:
untrimmed = untrimmed2 = 'unknown'
else:
untrimmed, untrimmed2 = open2(args.untrimmed_output,
args.untrimmed_paired_output)
out, out2 = open2(args.output, args.paired_output)
if out is None:
out = default_outfile
return OutputFiles(
rest=rest_file,
info=info_file,
wildcard=wildcard,
too_short=too_short,
too_short2=too_short2,
too_long=too_long,
too_long2=too_long2,
untrimmed=untrimmed,
untrimmed2=untrimmed2,
out=out,
out2=out2,
demultiplex=demultiplex or demultiplex_combinatorial,
interleaved=interleaved,
force_fasta=args.fasta,
)