def pipeline_from_parsed_args(options, paired, pair_filter_mode, quality_filename, is_interleaved_output):
"""
Setup a processing pipeline from parsed command-line options.
If there are any problems parsing the arguments, a CommandLineError is thrown.
Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)
"""
if not paired:
if options.untrimmed_paired_output:
raise CommandLineError("Option --untrimmed-paired-output can only be used when "
"trimming paired-end reads (with option -p).")
if paired:
if not is_interleaved_output:
if not options.paired_output:
raise CommandLineError("When paired-end trimming is enabled via -A/-G/-B/-U, "
"a second output file needs to be specified via -p (--paired-output).")
if not options.output:
raise CommandLineError("When you use -p or --paired-output, you must also "
"use the -o option.")
if bool(options.untrimmed_output) != bool(options.untrimmed_paired_output):
raise CommandLineError("When trimming paired-end reads, you must use either none "
"or both of the --untrimmed-output/--untrimmed-paired-output options.")
if options.too_short_output and not options.too_short_paired_output:
raise CommandLineError("When using --too-short-output with paired-end "
"reads, you also need to use --too-short-paired-output")
if options.too_long_output and not options.too_long_paired_output:
raise CommandLineError("When using --too-long-output with paired-end "
"reads, you also need to use --too-long-paired-output")
elif quality_filename is not None:
if options.format is not None:
raise CommandLineError('If a pair of .fasta and .qual files is given, the -f/--format '
'parameter cannot be used.')
if options.format is not None and options.format.lower() not in ['fasta', 'fastq', 'sra-fastq']:
raise CommandLineError("The input file format must be either 'fasta', 'fastq' or "
"'sra-fastq' (not '{0}').".format(options.format))
if options.maq:
options.colorspace = True
options.double_encode = True
options.trim_primer = True
options.strip_suffix.append('_F3')
options.suffix = "/1"
if options.zero_cap is None:
options.zero_cap = options.colorspace
if options.trim_primer and not options.colorspace:
raise CommandLineError("Trimming the primer makes only sense in colorspace.")
if options.double_encode and not options.colorspace:
raise CommandLineError("Double-encoding makes only sense in colorspace.")
if options.anywhere and options.colorspace:
raise CommandLineError("Using --anywhere with colorspace reads is currently not supported "
"(if you think this may be useful, contact the author).")
if not (0 <= options.error_rate <= 1.):
raise CommandLineError("The maximum error rate must be between 0 and 1.")
if options.overlap < 1:
raise CommandLineError("The overlap must be at least 1.")
if not (0 <= options.gc_content <= 100):
raise CommandLineError("GC content must be given as percentage between 0 and 100")
if options.action == 'none':
options.action = None
if options.colorspace:
if options.match_read_wildcards:
raise CommandLineError('IUPAC wildcards not supported in colorspace')
options.match_adapter_wildcards = False
adapter_parser = AdapterParser(
colorspace=options.colorspace,
max_error_rate=options.error_rate,
min_overlap=options.overlap,
read_wildcards=options.match_read_wildcards,
adapter_wildcards=options.match_adapter_wildcards,
indels=options.indels)
try:
adapters = adapter_parser.parse_multi(options.adapters, options.anywhere, options.front)
adapters2 = adapter_parser.parse_multi(options.adapters2, options.anywhere2, options.front2)
except IOError as e:
if e.errno == errno.ENOENT:
raise CommandLineError(e)
raise
except ValueError as e:
raise CommandLineError(e)
if options.debug:
for adapter in adapters + adapters2:
adapter.enable_debug()
# Create the processing pipeline.
# If no second-read adapters were given (via -A/-G/-B/-U), we need to
# be backwards compatible and *no modifications* are done to the second read.
if paired:
pipeline = PairedEndPipeline(pair_filter_mode, modify_first_read_only=paired == 'first')
else:
pipeline = SingleEndPipeline()
if options.cut:
if len(options.cut) > 2:
raise CommandLineError("You cannot remove bases from more than two ends.")
if len(options.cut) == 2 and options.cut[0] * options.cut[1] > 0:
raise CommandLineError("You cannot remove bases from the same end twice.")
for cut in options.cut:
if cut != 0:
pipeline.add1(UnconditionalCutter(cut))
if options.cut2:
if len(options.cut2) > 2:
raise CommandLineError("You cannot remove bases from more than two ends.")
if len(options.cut2) == 2 and options.cut2[0] * options.cut2[1] > 0:
raise CommandLineError("You cannot remove bases from the same end twice.")
for cut in options.cut2:
if cut != 0:
pipeline.add2(UnconditionalCutter(cut))
if options.nextseq_trim is not None:
pipeline.add(NextseqQualityTrimmer(options.nextseq_trim, options.quality_base))
if options.quality_cutoff is not None:
cutoffs = parse_cutoffs(options.quality_cutoff)
pipeline.add(QualityTrimmer(cutoffs[0], cutoffs[1], options.quality_base))
if adapters:
adapter_cutter = AdapterCutter(adapters, options.times, options.action)
pipeline.add1(adapter_cutter)
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, options.times, options.action)
pipeline.add2(adapter_cutter2)
# Modifiers that apply to both reads of paired-end reads unless in legacy mode
if options.length is not None:
pipeline.add(Shortener(options.length))
if options.trim_n:
pipeline.add(NEndTrimmer())
if options.length_tag:
pipeline.add(LengthTagModifier(options.length_tag))
if options.strip_f3:
options.strip_suffix.append('_F3')
for suffix in options.strip_suffix:
pipeline.add(SuffixRemover(suffix))
if options.prefix or options.suffix:
pipeline.add(PrefixSuffixAdder(options.prefix, options.suffix))
if options.double_encode:
pipeline.add(DoubleEncoder())
if options.zero_cap:
pipeline.add(ZeroCapper(quality_base=options.quality_base))
if options.trim_primer:
pipeline.add(PrimerTrimmer())
# Set filtering parameters
# Minimum/maximum length
for attr in 'minimum_length', 'maximum_length':
param = getattr(options, attr)
if param is not None:
lengths = parse_lengths(param)
if not paired and len(lengths) == 2:
raise CommandLineError('Two minimum or maximum lengths given for single-end data')
if paired and len(lengths) == 1:
lengths = (lengths[0], lengths[0])
setattr(pipeline, attr, lengths)
pipeline.max_n = options.max_n
pipeline.discard_casava = options.discard_casava
pipeline.discard_trimmed = options.discard_trimmed
pipeline.discard_untrimmed = options.discard_untrimmed
return pipeline
def pipeline_from_parsed_args(args, paired, file_opener, adapters,
adapters2) -> Pipeline:
"""
Setup a processing pipeline from parsed command-line arguments.
If there are any problems parsing the arguments, a CommandLineError is raised.
Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)
"""
if args.action == 'none':
args.action = None
# Create the processing pipeline
if paired:
pair_filter_mode = 'any' if args.pair_filter is None else args.pair_filter
pipeline = PairedEndPipeline(pair_filter_mode,
file_opener) # type: Any
else:
pipeline = SingleEndPipeline(file_opener)
# When adapters are being trimmed only in R1 or R2, override the pair filter mode
# as using the default of 'any' would regard all read pairs as untrimmed.
if isinstance(pipeline,
PairedEndPipeline) and (not adapters2 or not adapters) and (
args.discard_untrimmed or args.untrimmed_output
or args.untrimmed_paired_output):
pipeline.override_untrimmed_pair_filter = True
add_unconditional_cutters(pipeline, args.cut, args.cut2, paired)
pipeline_add = pipeline.add_both if paired else pipeline.add
if args.nextseq_trim is not None:
pipeline_add(
NextseqQualityTrimmer(args.nextseq_trim, args.quality_base))
if args.quality_cutoff is not None:
cutoffs = parse_cutoffs(args.quality_cutoff)
pipeline_add(QualityTrimmer(cutoffs[0], cutoffs[1], args.quality_base))
add_adapter_cutter(
pipeline,
adapters,
adapters2,
paired,
args.pair_adapters,
args.action,
args.times,
args.reverse_complement,
args.index,
)
for modifier in modifiers_applying_to_both_ends_if_paired(args):
pipeline_add(modifier)
# Set filtering parameters
# Minimum/maximum length
for attr in 'minimum_length', 'maximum_length':
param = getattr(args, attr)
if param is not None:
lengths = parse_lengths(param)
if not paired and len(lengths) == 2:
raise CommandLineError(
'Two minimum or maximum lengths given for single-end data')
if paired and len(lengths) == 1:
lengths = (lengths[0], lengths[0])
setattr(pipeline, attr, lengths)
pipeline.max_n = args.max_n
pipeline.max_expected_errors = args.max_expected_errors
pipeline.discard_casava = args.discard_casava
pipeline.discard_trimmed = args.discard_trimmed
pipeline.discard_untrimmed = args.discard_untrimmed
return pipeline
def pipeline_from_parsed_args(args, paired, is_interleaved_output):
"""
Setup a processing pipeline from parsed command-line arguments.
If there are any problems parsing the arguments, a CommandLineError is raised.
Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)
"""
check_arguments(args, paired, is_interleaved_output)
if args.action == 'none':
args.action = None
adapter_parser = AdapterParser(
max_error_rate=args.error_rate,
min_overlap=args.overlap,
read_wildcards=args.match_read_wildcards,
adapter_wildcards=args.match_adapter_wildcards,
indels=args.indels,
)
try:
adapters = adapter_parser.parse_multi(args.adapters)
adapters2 = adapter_parser.parse_multi(args.adapters2)
except (FileNotFoundError, ValueError) as e:
raise CommandLineError(e)
warn_duplicate_adapters(adapters)
warn_duplicate_adapters(adapters2)
if args.debug:
for adapter in adapters + adapters2:
adapter.enable_debug()
# Create the processing pipeline
if paired:
pair_filter_mode = 'any' if args.pair_filter is None else args.pair_filter
pipeline = PairedEndPipeline(pair_filter_mode)
else:
pipeline = SingleEndPipeline()
# When adapters are being trimmed only in R1 or R2, override the pair filter mode
# as using the default of 'any' would regard all read pairs as untrimmed.
if paired and (not adapters2
or not adapters) and (args.discard_untrimmed
or args.untrimmed_output
or args.untrimmed_paired_output):
pipeline.override_untrimmed_pair_filter = True
add_unconditional_cutters(pipeline, args.cut, args.cut2, paired)
pipeline_add = pipeline.add_both if paired else pipeline.add
if args.nextseq_trim is not None:
pipeline_add(
NextseqQualityTrimmer(args.nextseq_trim, args.quality_base))
if args.quality_cutoff is not None:
cutoffs = parse_cutoffs(args.quality_cutoff)
pipeline_add(QualityTrimmer(cutoffs[0], cutoffs[1], args.quality_base))
if args.pair_adapters:
try:
cutter = PairedAdapterCutter(adapters, adapters2, args.action)
except PairedAdapterCutterError as e:
raise CommandLineError("--pair-adapters: " + str(e))
pipeline.add_paired_modifier(cutter)
else:
adapter_cutter, adapter_cutter2 = None, None
if adapters:
adapter_cutter = AdapterCutter(adapters, args.times, args.action)
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, args.times, args.action)
if paired:
if adapter_cutter or adapter_cutter2:
pipeline.add(adapter_cutter, adapter_cutter2)
else:
if adapter_cutter:
pipeline.add(adapter_cutter)
for modifier in modifiers_applying_to_both_ends_if_paired(args):
pipeline_add(modifier)
# Set filtering parameters
# Minimum/maximum length
for attr in 'minimum_length', 'maximum_length':
param = getattr(args, attr)
if param is not None:
lengths = parse_lengths(param)
if not paired and len(lengths) == 2:
raise CommandLineError(
'Two minimum or maximum lengths given for single-end data')
if paired and len(lengths) == 1:
lengths = (lengths[0], lengths[0])
setattr(pipeline, attr, lengths)
pipeline.max_n = args.max_n
pipeline.discard_casava = args.discard_casava
pipeline.discard_trimmed = args.discard_trimmed
pipeline.discard_untrimmed = args.discard_untrimmed
return pipeline
def pipeline_from_parsed_args(args, paired, is_interleaved_output):
"""
Setup a processing pipeline from parsed command-line arguments.
If there are any problems parsing the arguments, a CommandLineError is thrown.
Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)
"""
if not paired:
if args.untrimmed_paired_output:
raise CommandLineError(
"Option --untrimmed-paired-output can only be used when "
"trimming paired-end reads (with option -p).")
if paired:
if not is_interleaved_output:
if not args.paired_output:
raise CommandLineError(
"When a paired-end trimming option such as -A/-G/-B/-U, "
"is used, a second output file needs to be specified via -p (--paired-output)."
)
if not args.output:
raise CommandLineError(
"When you use -p or --paired-output, you must also "
"use the -o option.")
if bool(args.untrimmed_output) != bool(args.untrimmed_paired_output):
raise CommandLineError(
"When trimming paired-end reads, you must use either none "
"or both of the --untrimmed-output/--untrimmed-paired-output options."
)
if args.too_short_output and not args.too_short_paired_output:
raise CommandLineError(
"When using --too-short-output with paired-end "
"reads, you also need to use --too-short-paired-output")
if args.too_long_output and not args.too_long_paired_output:
raise CommandLineError(
"When using --too-long-output with paired-end "
"reads, you also need to use --too-long-paired-output")
if args.format is not None:
logger.warning(
"Option --format is deprecated and ignored because the input file format is "
"always auto-detected")
if not (0 <= args.error_rate < 1.):
raise CommandLineError(
"The maximum error rate must be at least 0 and less than 1.")
if args.overlap < 1:
raise CommandLineError("The overlap must be at least 1.")
if not (0 <= args.gc_content <= 100):
raise CommandLineError(
"GC content must be given as percentage between 0 and 100")
if args.action == 'none':
args.action = None
adapter_parser = AdapterParser(
max_error_rate=args.error_rate,
min_overlap=args.overlap,
read_wildcards=args.match_read_wildcards,
adapter_wildcards=args.match_adapter_wildcards,
indels=args.indels,
)
try:
adapters = adapter_parser.parse_multi(args.adapters, args.anywhere,
args.front)
adapters2 = adapter_parser.parse_multi(args.adapters2, args.anywhere2,
args.front2)
except IOError as e:
if e.errno == errno.ENOENT:
raise CommandLineError(e)
raise
except ValueError as e:
raise CommandLineError(e)
if args.debug:
for adapter in adapters + adapters2:
adapter.enable_debug()
# Create the processing pipeline
if paired:
pair_filter_mode = 'any' if args.pair_filter is None else args.pair_filter
pipeline = PairedEndPipeline(pair_filter_mode)
else:
pipeline = SingleEndPipeline()
# When adapters are being trimmed only in R1 or R2, override the pair filter mode
# as using the default of 'any' would regard all read pairs as untrimmed.
if paired and (not adapters2
or not adapters) and (args.discard_untrimmed
or args.untrimmed_output
or args.untrimmed_paired_output):
pipeline.override_untrimmed_pair_filter = True
for i, cut_arg in enumerate([args.cut, args.cut2]):
# cut_arg is a list
if not cut_arg:
continue
if len(cut_arg) > 2:
raise CommandLineError(
"You cannot remove bases from more than two ends.")
if len(cut_arg) == 2 and cut_arg[0] * cut_arg[1] > 0:
raise CommandLineError(
"You cannot remove bases from the same end twice.")
for c in cut_arg:
if c == 0:
continue
if i == 0: # R1
if paired:
pipeline.add(UnconditionalCutter(c), None)
else:
pipeline.add(UnconditionalCutter(c))
else:
# R2
assert isinstance(pipeline, PairedEndPipeline)
pipeline.add(None, UnconditionalCutter(c))
pipeline_add = pipeline.add_both if paired else pipeline.add
if args.nextseq_trim is not None:
pipeline_add(
NextseqQualityTrimmer(args.nextseq_trim, args.quality_base))
if args.quality_cutoff is not None:
cutoffs = parse_cutoffs(args.quality_cutoff)
pipeline_add(QualityTrimmer(cutoffs[0], cutoffs[1], args.quality_base))
if args.pair_adapters:
if not paired:
raise CommandLineError(
"Option --pair-adapters can only be used when trimming "
"paired-end reads")
if args.times != 1:
raise CommandLineError(
"--pair-adapters cannot be used with --times")
try:
cutter = PairedAdapterCutter(adapters, adapters2, args.action)
except PairedAdapterCutterError as e:
raise CommandLineError("--pair-adapters: " + str(e))
pipeline.add_paired_modifier(cutter)
else:
adapter_cutter, adapter_cutter2 = None, None
if adapters:
adapter_cutter = AdapterCutter(adapters, args.times, args.action)
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, args.times, args.action)
if paired:
if adapter_cutter or adapter_cutter2:
pipeline.add(adapter_cutter, adapter_cutter2)
else:
if adapter_cutter:
pipeline.add(adapter_cutter)
# Remaining modifiers that apply to both reads of paired-end reads
if args.length is not None:
pipeline_add(Shortener(args.length))
if args.trim_n:
pipeline_add(NEndTrimmer())
if args.length_tag:
pipeline_add(LengthTagModifier(args.length_tag))
for suffix in args.strip_suffix:
pipeline_add(SuffixRemover(suffix))
if args.prefix or args.suffix:
pipeline_add(PrefixSuffixAdder(args.prefix, args.suffix))
if args.zero_cap:
pipeline_add(ZeroCapper(quality_base=args.quality_base))
# Set filtering parameters
# Minimum/maximum length
for attr in 'minimum_length', 'maximum_length':
param = getattr(args, attr)
if param is not None:
lengths = parse_lengths(param)
if not paired and len(lengths) == 2:
raise CommandLineError(
'Two minimum or maximum lengths given for single-end data')
if paired and len(lengths) == 1:
lengths = (lengths[0], lengths[0])
setattr(pipeline, attr, lengths)
pipeline.max_n = args.max_n
pipeline.discard_casava = args.discard_casava
pipeline.discard_trimmed = args.discard_trimmed
pipeline.discard_untrimmed = args.discard_untrimmed
return pipeline
def pipeline_from_parsed_args(args, paired, is_interleaved_output):
"""
Setup a processing pipeline from parsed command-line arguments.
If there are any problems parsing the arguments, a CommandLineError is thrown.
Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)
"""
check_arguments(args, paired, is_interleaved_output)
if args.action == 'none':
args.action = None
adapter_parser = AdapterParser(
max_error_rate=args.error_rate,
min_overlap=args.overlap,
read_wildcards=args.match_read_wildcards,
adapter_wildcards=args.match_adapter_wildcards,
indels=args.indels,
)
try:
adapters = adapter_parser.parse_multi(args.adapters, args.anywhere, args.front)
adapters2 = adapter_parser.parse_multi(args.adapters2, args.anywhere2, args.front2)
except IOError as e:
if e.errno == errno.ENOENT:
raise CommandLineError(e)
raise
except ValueError as e:
raise CommandLineError(e)
if args.debug:
for adapter in adapters + adapters2:
adapter.enable_debug()
# Create the processing pipeline
if paired:
pair_filter_mode = 'any' if args.pair_filter is None else args.pair_filter
pipeline = PairedEndPipeline(pair_filter_mode)
else:
pipeline = SingleEndPipeline()
# When adapters are being trimmed only in R1 or R2, override the pair filter mode
# as using the default of 'any' would regard all read pairs as untrimmed.
if paired and (not adapters2 or not adapters) and (
args.discard_untrimmed or args.untrimmed_output or args.untrimmed_paired_output):
pipeline.override_untrimmed_pair_filter = True
for i, cut_arg in enumerate([args.cut, args.cut2]):
# cut_arg is a list
if not cut_arg:
continue
if len(cut_arg) > 2:
raise CommandLineError("You cannot remove bases from more than two ends.")
if len(cut_arg) == 2 and cut_arg[0] * cut_arg[1] > 0:
raise CommandLineError("You cannot remove bases from the same end twice.")
for c in cut_arg:
if c == 0:
continue
if i == 0: # R1
if paired:
pipeline.add(UnconditionalCutter(c), None)
else:
pipeline.add(UnconditionalCutter(c))
else:
# R2
assert isinstance(pipeline, PairedEndPipeline)
pipeline.add(None, UnconditionalCutter(c))
pipeline_add = pipeline.add_both if paired else pipeline.add
if args.nextseq_trim is not None:
pipeline_add(NextseqQualityTrimmer(args.nextseq_trim, args.quality_base))
if args.quality_cutoff is not None:
cutoffs = parse_cutoffs(args.quality_cutoff)
pipeline_add(QualityTrimmer(cutoffs[0], cutoffs[1], args.quality_base))
if args.pair_adapters:
if not paired:
raise CommandLineError("Option --pair-adapters can only be used when trimming "
"paired-end reads")
if args.times != 1:
raise CommandLineError("--pair-adapters cannot be used with --times")
try:
cutter = PairedAdapterCutter(adapters, adapters2, args.action)
except PairedAdapterCutterError as e:
raise CommandLineError("--pair-adapters: " + str(e))
pipeline.add_paired_modifier(cutter)
else:
adapter_cutter, adapter_cutter2 = None, None
if adapters:
adapter_cutter = AdapterCutter(adapters, args.times, args.action)
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, args.times, args.action)
if paired:
if adapter_cutter or adapter_cutter2:
pipeline.add(adapter_cutter, adapter_cutter2)
else:
if adapter_cutter:
pipeline.add(adapter_cutter)
# Remaining modifiers that apply to both reads of paired-end reads
if args.length is not None:
pipeline_add(Shortener(args.length))
if args.trim_n:
pipeline_add(NEndTrimmer())
if args.length_tag:
pipeline_add(LengthTagModifier(args.length_tag))
for suffix in args.strip_suffix:
pipeline_add(SuffixRemover(suffix))
if args.prefix or args.suffix:
pipeline_add(PrefixSuffixAdder(args.prefix, args.suffix))
if args.zero_cap:
pipeline_add(ZeroCapper(quality_base=args.quality_base))
# Set filtering parameters
# Minimum/maximum length
for attr in 'minimum_length', 'maximum_length':
param = getattr(args, attr)
if param is not None:
lengths = parse_lengths(param)
if not paired and len(lengths) == 2:
raise CommandLineError('Two minimum or maximum lengths given for single-end data')
if paired and len(lengths) == 1:
lengths = (lengths[0], lengths[0])
setattr(pipeline, attr, lengths)
pipeline.max_n = args.max_n
pipeline.discard_casava = args.discard_casava
pipeline.discard_trimmed = args.discard_trimmed
pipeline.discard_untrimmed = args.discard_untrimmed
return pipeline