def test_paired_adapter_cutter_actions(action, expected_trimmed1,
expected_trimmed2):
a1 = BackAdapter("GGTTAA")
a2 = BackAdapter("AACCGG")
s1 = Sequence("name", "CCCCGGTTAACCCC")
s2 = Sequence("name", "TTTTAACCGGTTTT")
pac = PairedAdapterCutter([a1], [a2], action=action)
info1 = ModificationInfo(s1)
info2 = ModificationInfo(s2)
trimmed1, trimmed2 = pac(s1, s2, info1, info2)
assert expected_trimmed1 == trimmed1.sequence
assert expected_trimmed2 == trimmed2.sequence
def test_paired_adapter_cutter_actions(action, expected_trimmed1,
expected_trimmed2):
from cutadapt.adapters import SingleAdapter, Where
a1 = SingleAdapter("GGTTAA", where=Where.BACK)
a2 = SingleAdapter("AACCGG", where=Where.BACK)
s1 = Sequence("name", "CCCCGGTTAACCCC")
s2 = Sequence("name", "TTTTAACCGGTTTT")
pac = PairedAdapterCutter([a1], [a2], action=action)
info1 = ModificationInfo()
info2 = ModificationInfo()
trimmed1, trimmed2 = pac(s1, s2, info1, info2)
assert expected_trimmed1 == trimmed1.sequence
assert expected_trimmed2 == trimmed2.sequence
def add_adapter_cutter(
pipeline,
adapters,
adapters2,
paired: bool,
pair_adapters: bool,
action: Optional[str],
times: int,
reverse_complement: bool,
add_rc_suffix: bool,
allow_index: bool,
):
if pair_adapters:
if reverse_complement:
raise CommandLineError("Cannot use --revcomp with --pair-adapters")
try:
cutter = PairedAdapterCutter(adapters, adapters2, action)
except PairedAdapterCutterError as e:
raise CommandLineError("--pair-adapters: " + str(e))
pipeline.add_paired_modifier(cutter)
else:
adapter_cutter, adapter_cutter2 = None, None
try:
if adapters:
adapter_cutter = AdapterCutter(adapters, times, action, allow_index)
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, times, action, allow_index)
except ValueError as e:
raise CommandLineError(e)
if paired:
if reverse_complement:
raise CommandLineError("--revcomp not implemented for paired-end reads")
if adapter_cutter or adapter_cutter2:
pipeline.add(adapter_cutter, adapter_cutter2)
elif adapter_cutter:
if reverse_complement:
modifier = ReverseComplementer(
adapter_cutter,
rc_suffix=" rc" if add_rc_suffix else None,
) # type: Union[AdapterCutter,ReverseComplementer]
else:
modifier = adapter_cutter
pipeline.add(modifier)
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 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)
"""
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