def collect(back, anywhere, front):
adapters = []
for name, seq, where in gather_adapters(back, anywhere, front):
if not seq:
parser.error("The adapter sequence is empty.")
adapter = ADAPTER_CLASS(seq, where, options.error_rate,
options.overlap, options.match_read_wildcards,
options.match_adapter_wildcards, name=name, indels=options.indels)
if options.debug:
adapter.enable_debug()
adapters.append(adapter)
return adapters
def collect(back, anywhere, front):
adapters = []
for name, seq, where in gather_adapters(back, anywhere, front):
if not seq:
parser.error("The adapter sequence is empty.")
if not options.indels and where not in (PREFIX, SUFFIX):
parser.error("Not allowing indels is currently supported only for anchored 5' and 3' adapters.")
adapter = ADAPTER_CLASS(seq, where, options.error_rate,
options.overlap, options.match_read_wildcards,
options.match_adapter_wildcards, name=name, indels=options.indels)
adapters.append(adapter)
return adapters
def collect(back, anywhere, front):
adapters = []
for name, seq, where in gather_adapters(back, anywhere, front):
if not seq:
parser.error("The adapter sequence is empty.")
adapter = ADAPTER_CLASS(seq,
where,
options.error_rate,
options.overlap,
options.match_read_wildcards,
options.match_adapter_wildcards,
name=name,
indels=options.indels)
if options.debug:
adapter.enable_debug()
adapters.append(adapter)
return adapters
def __init__(self, queue=None, results=None, adapter=None, phred64=False):
super(Worker, self).__init__()
self.queue=queue
self.results = results
self.phred = 64 if phred64 else 33
self.modifiers = [QualityTrimmer(0, 10, self.phred)]
self.adapters = []
self.error_rate = 0.12
self.min_length = 16
if adapter.startswith('+'):
self.modifiers.append(UnconditionalCutter(int(adapter)))
elif adapter == 'none':
self.adapter = None
else:
for name,seq,where in gather_adapters(adapter.split(','), [], []):
self.adapters.append(Adapter(seq, where, self.error_rate, name=name))
adapter_cutter = AdapterCutter(self.adapters)
self.modifiers.append(adapter_cutter)
def main(cmdlineargs=None, default_outfile=sys.stdout):
"""
Main function that evaluates command-line parameters and iterates
over all reads.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
parser = get_option_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
options, args = parser.parse_args(args=cmdlineargs)
if len(args) == 0:
parser.error("At least one parameter needed: name of a FASTA or FASTQ file.")
elif len(args) > 2:
parser.error("Too many parameters.")
input_filename = args[0]
# If a second file name was given, then we either have single-end reads
# provided as a pair of .fasta/.qual files or we have paired-end reads.
quality_filename = None
input_paired_filename = None
if len(args) == 2:
if args[0].endswith(".qual"):
parser.error("The QUAL file must be the second argument.")
if args[1].endswith(".qual"):
quality_filename = args[1]
else:
input_paired_filename = args[1]
if not options.paired_output:
parser.error("You must use --paired-output when trimming paired-end reads.")
if len(args) == 1 and options.paired_output:
parser.error("You specified a --paired-output file, but gave only one input file.")
if options.paired_output and bool(options.untrimmed_output) != bool(options.untrimmed_paired_output):
parser.error(
"When trimming paired-end reads, you must use either none "
"or both of the --untrimmed-output/--untrimmed-paired-output options."
)
if options.untrimmed_paired_output and not options.paired_output:
parser.error(
"Option --untrimmed-paired-output can only be used when "
"trimming paired-end reads (with option --paired-output)."
)
if input_filename.endswith(".qual"):
parser.error("Need a FASTA file in addition to the QUAL file.")
if options.format is not None and options.format.lower() not in ["fasta", "fastq", "sra-fastq"]:
parser.error(
"The input file format must be either 'fasta', 'fastq' or "
"'sra-fastq' (not '{0}').".format(options.format)
)
# TODO should this really be an error?
if options.format is not None and quality_filename is not None:
parser.error("If a pair of .fasta and .qual files is given, the -f/--format parameter cannot be used.")
writers = []
too_short_outfile = None # too short reads go here
too_short_filter = None
# TODO pass file name to TooShortReadFilter, add a .close() method?
if options.minimum_length > 0:
if options.too_short_output:
too_short_outfile = xopen(options.too_short_output, "w")
else:
too_short_outfile = None
too_short_filter = TooShortReadFilter(options.minimum_length, too_short_outfile)
writers.append(too_short_filter)
too_long_outfile = None # too long reads go here
too_long_filter = None
if options.maximum_length < sys.maxsize:
if options.too_long_output is not None:
too_long_outfile = xopen(options.too_long_output, "w")
else:
too_long_outfile = None
too_long_filter = TooLongReadFilter(options.maximum_length, too_long_outfile)
writers.append(too_long_filter)
demultiplexer = None
if options.output is not None and "{name}" in options.output:
if options.discard_trimmed:
parser.error("Do not use --discard-trimmed when demultiplexing.")
if input_paired_filename:
parser.error("Demultiplexing not supported for paired-end files, yet.")
untrimmed = options.output.format(name="unknown")
if options.untrimmed_output:
untrimmed = options.untrimmed_output
if options.discard_untrimmed:
untrimmed = None
demultiplexer = Demultiplexer(options.output, untrimmed)
writers.append(demultiplexer)
trimmed_outfile, untrimmed_outfile = None, None
trimmed_paired_outfile, untrimmed_paired_outfile = None, None
else:
trimmed_outfile, untrimmed_outfile = trimmed_and_untrimmed_files(
default_outfile,
options.output,
options.untrimmed_output,
options.discard_trimmed,
options.discard_untrimmed,
)
trimmed_paired_outfile, untrimmed_paired_outfile = trimmed_and_untrimmed_files(
None, # applies when not trimming paired-end data
options.paired_output,
options.untrimmed_paired_output,
options.discard_trimmed,
options.discard_untrimmed,
)
writer = ProcessedReadWriter(
trimmed_outfile, trimmed_paired_outfile, untrimmed_outfile, untrimmed_paired_outfile
)
writers.append(writer)
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:
parser.error("Trimming the primer makes only sense in colorspace.")
if options.double_encode and not options.colorspace:
parser.error("Double-encoding makes only sense in colorspace.")
if options.anywhere and options.colorspace:
parser.error(
"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 <= 1.0):
parser.error("The maximum error rate must be between 0 and 1.")
if options.overlap < 1:
parser.error("The overlap must be at least 1.")
if options.rest_file is not None:
options.rest_file = xopen(options.rest_file, "w")
rest_writer = RestFileWriter(options.rest_file)
else:
rest_writer = None
if options.info_file is not None:
options.info_file = xopen(options.info_file, "w")
if options.wildcard_file is not None:
options.wildcard_file = xopen(options.wildcard_file, "w")
if options.colorspace:
if options.match_read_wildcards:
parser.error("IUPAC wildcards not supported in colorspace")
options.match_adapter_wildcards = False
adapters = []
ADAPTER_CLASS = ColorspaceAdapter if options.colorspace else Adapter
try:
for name, seq, where in gather_adapters(options.adapters, options.anywhere, options.front):
if not seq:
parser.error("The adapter sequence is empty")
if not options.indels and where not in (PREFIX, SUFFIX):
parser.error("Not allowing indels is currently supported only for anchored 5' and 3' adapters.")
adapter = ADAPTER_CLASS(
seq,
where,
options.error_rate,
options.overlap,
options.match_read_wildcards,
options.match_adapter_wildcards,
name=name,
indels=options.indels,
)
adapters.append(adapter)
except IOError as e:
if e.errno == errno.ENOENT:
print("Error:", e, file=sys.stderr)
sys.exit(1)
raise
if (
not adapters
and options.quality_cutoff == 0
and options.cut == 0
and options.minimum_length == 0
and options.maximum_length == sys.maxsize
):
parser.error("You need to provide at least one adapter sequence.")
if input_paired_filename:
reader = seqio.PairedSequenceReader(
input_filename, input_paired_filename, colorspace=options.colorspace, fileformat=options.format
)
else:
reader = read_sequences(
input_filename, quality_filename, colorspace=options.colorspace, fileformat=options.format
)
# Create the processing pipeline as a list of "modifiers".
modifiers = []
if options.cut:
if len(options.cut) > 2:
parser.error("You cannot remove bases from more than two ends.")
if len(options.cut) == 2 and options.cut[0] * options.cut[1] > 0:
parser.error("You cannot remove bases from the same end twice.")
for cut in options.cut:
if cut != 0:
modifiers.append(UnconditionalCutter(cut))
if options.quality_cutoff > 0:
modifiers.append(QualityTrimmer(options.quality_cutoff, options.quality_base))
if adapters:
adapter_cutter = AdapterCutter(
adapters, options.times, options.wildcard_file, options.info_file, rest_writer, options.action
)
modifiers.append(adapter_cutter)
else:
adapter_cutter = None
if options.length_tag:
modifiers.append(LengthTagModifier(options.length_tag))
if options.strip_f3:
options.strip_suffix.append("_F3")
for suffix in options.strip_suffix:
modifiers.append(SuffixRemover(suffix))
if options.prefix or options.suffix:
modifiers.append(PrefixSuffixAdder(options.prefix, options.suffix))
if options.double_encode:
modifiers.append(DoubleEncoder())
if options.zero_cap and reader.delivers_qualities:
modifiers.append(ZeroCapper(quality_base=options.quality_base))
if options.trim_primer:
modifiers.append(PrimerTrimmer)
start_time = time.clock()
try:
if input_paired_filename:
stats = process_paired_reads(reader, modifiers, writers)
else:
stats = process_single_reads(reader, modifiers, writers)
except KeyboardInterrupt as e:
print("Interrupted", file=sys.stderr)
sys.exit(1)
except IOError as e:
if e.errno == errno.EPIPE:
sys.exit(1)
raise
except seqio.FormatError as e:
print("Error:", e, file=sys.stderr)
sys.exit(1)
# close open files
for f in [
trimmed_outfile,
untrimmed_outfile,
trimmed_paired_outfile,
untrimmed_paired_outfile,
options.rest_file,
options.wildcard_file,
options.info_file,
too_short_outfile,
too_long_outfile,
options.info_file,
demultiplexer,
]:
if f is not None and f is not sys.stdin and f is not sys.stdout:
f.close()
if not options.quiet:
# send statistics to stderr if result was sent to stdout
stat_file = sys.stderr if options.output is None else None
print_statistics(
adapters,
time.clock() - start_time,
stats,
options.action,
adapter_cutter.reads_matched if adapter_cutter else 0,
options.error_rate,
too_short_filter.too_short if too_short_filter else 0,
too_long_filter.too_long if too_long_filter else 0,
cmdlineargs,
file=stat_file,
)
def main(cmdlineargs=None, default_outfile=sys.stdout):
"""
Main function that evaluates command-line parameters and iterates
over all reads.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
logging.basicConfig(level=logging.INFO, format='%(message)s') # %(levelname)s
parser = get_option_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
options, args = parser.parse_args(args=cmdlineargs)
if len(args) == 0:
parser.error("At least one parameter needed: name of a FASTA or FASTQ file.")
elif len(args) > 2:
parser.error("Too many parameters.")
input_filename = args[0]
# Find out which 'mode' we need to use.
# Default: single-read trimming (neither -p nor -A/-G/-B/-U given)
paired = False
if options.paired_output:
# Modify first read only, keep second in sync (-p given, but not -A/-G/-B/-U).
# This exists for backwards compatibility ('legacy mode').
paired = 'first'
if options.adapters2 or options.front2 or options.anywhere2 or options.cut2:
# Full paired-end trimming when both -p and -A/-G/-B/-U given
# Also the read modifications (such as quality trimming) are applied
# to second read.
paired = 'both'
if paired and len(args) == 1:
parser.error("When paired-end trimming is enabled via -A/-G/-B/-U or -p, "
"two input files are required.")
if paired:
input_paired_filename = args[1]
quality_filename = None
else:
input_paired_filename = None
if len(args) == 2:
if args[0].endswith('.qual'):
parser.error("The QUAL file must be the second argument.")
quality_filename = args[1]
else:
quality_filename = None
if paired:
if not options.paired_output:
parser.error("When paired-end trimming is enabled via -A/-G/-B/-U, "
"a second output file needs to be specified via -p (--paired-output).")
if bool(options.untrimmed_output) != bool(options.untrimmed_paired_output):
parser.error("When trimming paired-end reads, you must use either none "
"or both of the --untrimmed-output/--untrimmed-paired-output options.")
else:
if options.untrimmed_paired_output:
parser.error("Option --untrimmed-paired-output can only be used when "
"trimming paired-end reads (with option -p).")
if input_filename.endswith('.qual'):
parser.error("Need a FASTA file in addition to the QUAL file.")
if options.format is not None and quality_filename is not None:
parser.error("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']:
parser.error("The input file format must be either 'fasta', 'fastq' or "
"'sra-fastq' (not '{0}').".format(options.format))
if options.quality_cutoff is not None:
cutoffs = options.quality_cutoff.split(',')
if len(cutoffs) == 1:
try:
cutoffs = [0, int(cutoffs[0])]
except ValueError as e:
parser.error("Quality cutoff value not recognized: {0}".format(e))
elif len(cutoffs) == 2:
try:
cutoffs = [int(cutoffs[0]), int(cutoffs[1])]
except ValueError as e:
parser.error("Quality cutoff value not recognized: {0}".format(e))
else:
parser.error("Expected one value or two values separated by comma for the quality cutoff")
else:
cutoffs = None
writers = []
too_short_outfile = None # too short reads go here
too_short_filter = None
# TODO pass file name to TooShortReadFilter, add a .close() method?
if options.minimum_length > 0:
if options.too_short_output:
too_short_outfile = xopen(options.too_short_output, 'w')
else:
too_short_outfile = None
too_short_filter = TooShortReadFilter(options.minimum_length,
too_short_outfile, paired=='both')
writers.append(too_short_filter)
too_long_outfile = None # too long reads go here
too_long_filter = None
if options.maximum_length < sys.maxsize:
if options.too_long_output is not None:
too_long_outfile = xopen(options.too_long_output, 'w')
else:
too_long_outfile = None
too_long_filter = TooLongReadFilter(options.maximum_length,
too_long_outfile, check_second=paired=='both')
writers.append(too_long_filter)
if options.max_n != -1:
writers.append(NContentTrimmer(options.max_n, check_second=paired=='both'))
demultiplexer = None
if options.output is not None and '{name}' in options.output:
if options.discard_trimmed:
parser.error("Do not use --discard-trimmed when demultiplexing.")
if paired:
parser.error("Demultiplexing not supported for paired-end files, yet.")
untrimmed = options.output.format(name='unknown')
if options.untrimmed_output:
untrimmed = options.untrimmed_output
if options.discard_untrimmed:
untrimmed = None
demultiplexer = Demultiplexer(options.output, untrimmed)
writers.append(demultiplexer)
trimmed_outfile, untrimmed_outfile = None, None
trimmed_paired_outfile, untrimmed_paired_outfile = None, None
else:
trimmed_outfile, untrimmed_outfile = trimmed_and_untrimmed_files(
default_outfile,
options.output,
options.untrimmed_output,
options.discard_trimmed,
options.discard_untrimmed)
trimmed_paired_outfile, untrimmed_paired_outfile = trimmed_and_untrimmed_files(
None, # applies when not trimming paired-end data
options.paired_output,
options.untrimmed_paired_output,
options.discard_trimmed,
options.discard_untrimmed)
writer = ProcessedReadWriter(
trimmed_outfile, trimmed_paired_outfile,
untrimmed_outfile, untrimmed_paired_outfile,
check_second=paired=='both'
)
writers.append(writer)
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:
parser.error("Trimming the primer makes only sense in colorspace.")
if options.double_encode and not options.colorspace:
parser.error("Double-encoding makes only sense in colorspace.")
if options.anywhere and options.colorspace:
parser.error("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.):
parser.error("The maximum error rate must be between 0 and 1.")
if options.overlap < 1:
parser.error("The overlap must be at least 1.")
if options.rest_file is not None:
options.rest_file = xopen(options.rest_file, 'w')
rest_writer = RestFileWriter(options.rest_file)
else:
rest_writer = None
if options.info_file is not None:
options.info_file = xopen(options.info_file, 'w')
if options.wildcard_file is not None:
options.wildcard_file = xopen(options.wildcard_file, 'w')
if options.colorspace:
if options.match_read_wildcards:
parser.error('IUPAC wildcards not supported in colorspace')
options.match_adapter_wildcards = False
ADAPTER_CLASS = ColorspaceAdapter if options.colorspace else Adapter
try:
# TODO refactor, code duplicated
adapters = []
for name, seq, where in gather_adapters(options.adapters, options.anywhere, options.front):
if not seq:
parser.error("The adapter sequence is empty.")
if not options.indels and where not in (PREFIX, SUFFIX):
parser.error("Not allowing indels is currently supported only for anchored 5' and 3' adapters.")
adapter = ADAPTER_CLASS(seq, where, options.error_rate,
options.overlap, options.match_read_wildcards,
options.match_adapter_wildcards, name=name, indels=options.indels)
adapters.append(adapter)
adapters2 = []
for name, seq, where in gather_adapters(options.adapters2, options.anywhere2, options.front2):
if not seq:
parser.error("The adapter sequence is empty.")
if not options.indels and where != PREFIX:
parser.error("Not allowing indels is currently supported only for anchored 5' and 3' adapters.")
adapter = ADAPTER_CLASS(seq, where, options.error_rate,
options.overlap, options.match_read_wildcards,
options.match_adapter_wildcards, name=name, indels=options.indels)
adapters2.append(adapter)
except IOError as e:
if e.errno == errno.ENOENT:
parser.error(e)
raise
if not adapters and not adapters2 and not cutoffs and \
options.cut == [] and options.cut2 == [] and \
options.minimum_length == 0 and \
options.maximum_length == sys.maxsize and \
quality_filename is None and \
options.max_n == -1:
parser.error("You need to provide at least one adapter sequence.")
try:
reader = seqio.open(input_filename, file2=input_paired_filename,
qualfile=quality_filename, colorspace=options.colorspace,
fileformat=options.format)
except (seqio.UnknownFileType, IOError) as e:
parser.error(e)
# Create the processing pipeline consisting of a list of "modifiers".
modifiers = []
if options.cut:
if len(options.cut) > 2:
parser.error("You cannot remove bases from more than two ends.")
if len(options.cut) == 2 and options.cut[0] * options.cut[1] > 0:
parser.error("You cannot remove bases from the same end twice.")
for cut in options.cut:
if cut != 0:
modifiers.append(UnconditionalCutter(cut))
if cutoffs:
modifiers.append(QualityTrimmer(cutoffs[0], cutoffs[1], options.quality_base))
if adapters:
adapter_cutter = AdapterCutter(adapters, options.times,
options.wildcard_file, options.info_file,
rest_writer, options.action)
modifiers.append(adapter_cutter)
else:
adapter_cutter = None
# Modifiers that apply to both reads of paired-end reads
modifiers_both = []
if options.trim_n:
modifiers_both.append(NEndTrimmer())
if options.length_tag:
modifiers_both.append(LengthTagModifier(options.length_tag))
if options.strip_f3:
options.strip_suffix.append('_F3')
for suffix in options.strip_suffix:
modifiers_both.append(SuffixRemover(suffix))
if options.prefix or options.suffix:
modifiers_both.append(PrefixSuffixAdder(options.prefix, options.suffix))
if options.double_encode:
modifiers_both.append(DoubleEncoder())
if options.zero_cap and reader.delivers_qualities:
modifiers_both.append(ZeroCapper(quality_base=options.quality_base))
if options.trim_primer:
modifiers_both.append(PrimerTrimmer)
modifiers.extend(modifiers_both)
# For paired-end data, create a second processing pipeline.
# However, 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.
modifiers2 = []
if paired == 'both':
if options.cut2:
if len(options.cut2) > 2:
parser.error("You cannot remove bases from more than two ends.")
if len(options.cut2) == 2 and options.cut2[0] * options.cut2[1] > 0:
parser.error("You cannot remove bases from the same end twice.")
for cut in options.cut2:
if cut != 0:
modifiers2.append(UnconditionalCutter(cut))
if cutoffs:
modifiers2.append(QualityTrimmer(cutoffs[0], cutoffs[1], options.quality_base))
if adapters2:
adapter_cutter2 = AdapterCutter(adapters2, options.times,
None, None, None, options.action)
modifiers2.append(adapter_cutter2)
else:
adapter_cutter2 = None
modifiers2.extend(modifiers_both)
# Due to backwards compatibility, from here on logging output needs to be
# sent to standard output instead of standard error if the -o option is used.
if options.output:
logger.root.handlers = []
logging.basicConfig(level=logging.INFO, format='%(message)s', stream=sys.stdout)
logger.info("This is cutadapt %s with Python %s", __version__, platform.python_version())
logger.info("Command line parameters: %s", " ".join(cmdlineargs))
logger.info("Trimming %s adapter%s with at most %.1f%% errors in %s mode ...",
len(adapters) + len(adapters2), 's' if len(adapters) + len(adapters2) != 1 else '',
options.error_rate * 100,
{ False: 'single-end', 'first': 'paired-end legacy', 'both': 'paired-end' }[paired])
start_time = time.clock()
try:
if paired:
stats = process_paired_reads(reader, modifiers, modifiers2, writers)
else:
stats = process_single_reads(reader, modifiers, writers)
except KeyboardInterrupt as e:
print("Interrupted", file=sys.stderr)
sys.exit(130)
except IOError as e:
if e.errno == errno.EPIPE:
sys.exit(1)
raise
except (seqio.FormatError, EOFError) as e:
sys.exit("cutadapt: error: {0}".format(e))
# close open files
for f in [trimmed_outfile, untrimmed_outfile, trimmed_paired_outfile,
untrimmed_paired_outfile, options.rest_file, options.wildcard_file,
options.info_file, too_short_outfile, too_long_outfile,
options.info_file, demultiplexer]:
if f is not None and f is not sys.stdin and f is not sys.stdout:
f.close()
elapsed_time = time.clock() - start_time
if not options.quiet:
stats.collect((adapters, adapters2), elapsed_time,
modifiers, modifiers2, writers)
# send statistics to stderr if result was sent to stdout
stat_file = sys.stderr if options.output is None else None
with redirect_standard_output(stat_file):
print_report(stats, (adapters, adapters2))
def parse_adapters(adapter, error_rate=None):
adapters = []
for name, seq, where in gather_adapters(adapter.split(','), [], []):
adapters.append(Adapter(seq, where, error_rate, name=name))
return adapters
def main(cmdlineargs=None, default_outfile=sys.stdout):
"""
Main function that evaluates command-line parameters and iterates
over all reads.
default_outfile is the file to which trimmed reads are sent if the ``-o``
parameter is not used.
"""
parser = get_option_parser()
if cmdlineargs is None:
cmdlineargs = sys.argv[1:]
options, args = parser.parse_args(args=cmdlineargs)
if len(args) == 0:
parser.error(
"At least one parameter needed: name of a FASTA or FASTQ file.")
elif len(args) > 2:
parser.error("Too many parameters.")
input_filename = args[0]
# If a second file name was given, then we either have single-end reads
# provided as a pair of .fasta/.qual files or we have paired-end reads.
quality_filename = None
input_paired_filename = None
if len(args) == 2:
if args[0].endswith('.qual'):
parser.error("The QUAL file must be the second argument.")
if args[1].endswith('.qual'):
quality_filename = args[1]
else:
input_paired_filename = args[1]
if not options.paired_output:
parser.error(
'You must use --paired-output when trimming paired-end reads.'
)
if len(args) == 1 and options.paired_output:
parser.error(
"You specified a --paired-output file, but gave only one input file."
)
if options.paired_output and bool(options.untrimmed_output) != bool(
options.untrimmed_paired_output):
parser.error(
"When trimming paired-end reads, you must use either none "
"or both of the --untrimmed-output/--untrimmed-paired-output options."
)
if options.untrimmed_paired_output and not options.paired_output:
parser.error(
"Option --untrimmed-paired-output can only be used when "
"trimming paired-end reads (with option --paired-output).")
if input_filename.endswith('.qual'):
parser.error("Need a FASTA file in addition to the QUAL file.")
if options.format is not None and options.format.lower() not in [
'fasta', 'fastq', 'sra-fastq'
]:
parser.error(
"The input file format must be either 'fasta', 'fastq' or "
"'sra-fastq' (not '{0}').".format(options.format))
# TODO should this really be an error?
if options.format is not None and quality_filename is not None:
parser.error(
"If a pair of .fasta and .qual files is given, the -f/--format parameter cannot be used."
)
writers = []
too_short_outfile = None # too short reads go here
too_short_filter = None
# TODO pass file name to TooShortReadFilter, add a .close() method?
if options.minimum_length > 0:
if options.too_short_output:
too_short_outfile = xopen(options.too_short_output, 'w')
else:
too_short_outfile = None
too_short_filter = TooShortReadFilter(options.minimum_length,
too_short_outfile)
writers.append(too_short_filter)
too_long_outfile = None # too long reads go here
too_long_filter = None
if options.maximum_length < sys.maxsize:
if options.too_long_output is not None:
too_long_outfile = xopen(options.too_long_output, 'w')
else:
too_long_outfile = None
too_long_filter = TooLongReadFilter(options.maximum_length,
too_long_outfile)
writers.append(too_long_filter)
demultiplexer = None
if options.output is not None and '{name}' in options.output:
if options.discard_trimmed:
parser.error("Do not use --discard-trimmed when demultiplexing.")
if input_paired_filename:
parser.error(
"Demultiplexing not supported for paired-end files, yet.")
untrimmed = options.output.format(name='unknown')
if options.untrimmed_output:
untrimmed = options.untrimmed_output
if options.discard_untrimmed:
untrimmed = None
demultiplexer = Demultiplexer(options.output, untrimmed)
writers.append(demultiplexer)
trimmed_outfile, untrimmed_outfile = None, None
trimmed_paired_outfile, untrimmed_paired_outfile = None, None
else:
trimmed_outfile, untrimmed_outfile = trimmed_and_untrimmed_files(
default_outfile, options.output, options.untrimmed_output,
options.discard_trimmed, options.discard_untrimmed)
trimmed_paired_outfile, untrimmed_paired_outfile = trimmed_and_untrimmed_files(
None, # applies when not trimming paired-end data
options.paired_output,
options.untrimmed_paired_output,
options.discard_trimmed,
options.discard_untrimmed)
writer = ProcessedReadWriter(trimmed_outfile, trimmed_paired_outfile,
untrimmed_outfile,
untrimmed_paired_outfile)
writers.append(writer)
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:
parser.error("Trimming the primer makes only sense in colorspace.")
if options.double_encode and not options.colorspace:
parser.error("Double-encoding makes only sense in colorspace.")
if options.anywhere and options.colorspace:
parser.error(
"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.):
parser.error("The maximum error rate must be between 0 and 1.")
if options.overlap < 1:
parser.error("The overlap must be at least 1.")
if options.rest_file is not None:
options.rest_file = xopen(options.rest_file, 'w')
rest_writer = RestFileWriter(options.rest_file)
else:
rest_writer = None
if options.info_file is not None:
options.info_file = xopen(options.info_file, 'w')
if options.wildcard_file is not None:
options.wildcard_file = xopen(options.wildcard_file, 'w')
if options.colorspace:
if options.match_read_wildcards:
parser.error('IUPAC wildcards not supported in colorspace')
options.match_adapter_wildcards = False
adapters = []
ADAPTER_CLASS = ColorspaceAdapter if options.colorspace else Adapter
try:
for name, seq, where in gather_adapters(options.adapters,
options.anywhere,
options.front):
if not seq:
parser.error("The adapter sequence is empty")
if not options.indels and where not in (PREFIX, SUFFIX):
parser.error(
"Not allowing indels is currently supported only for anchored 5' and 3' adapters."
)
adapter = ADAPTER_CLASS(seq,
where,
options.error_rate,
options.overlap,
options.match_read_wildcards,
options.match_adapter_wildcards,
name=name,
indels=options.indels)
adapters.append(adapter)
except IOError as e:
if e.errno == errno.ENOENT:
print("Error:", e, file=sys.stderr)
sys.exit(1)
raise
if not adapters and options.quality_cutoff == 0 and options.cut == 0 and \
options.minimum_length == 0 and options.maximum_length == sys.maxsize:
parser.error("You need to provide at least one adapter sequence.")
if input_paired_filename:
reader = seqio.PairedSequenceReader(input_filename,
input_paired_filename,
colorspace=options.colorspace,
fileformat=options.format)
else:
reader = read_sequences(input_filename,
quality_filename,
colorspace=options.colorspace,
fileformat=options.format)
# Create the processing pipeline as a list of "modifiers".
modifiers = []
if options.cut:
if len(options.cut) > 2:
parser.error("You cannot remove bases from more than two ends.")
if len(options.cut) == 2 and options.cut[0] * options.cut[1] > 0:
parser.error("You cannot remove bases from the same end twice.")
for cut in options.cut:
if cut != 0:
modifiers.append(UnconditionalCutter(cut))
if options.quality_cutoff > 0:
modifiers.append(
QualityTrimmer(options.quality_cutoff, options.quality_base))
if adapters:
adapter_cutter = AdapterCutter(adapters, options.times,
options.wildcard_file,
options.info_file, rest_writer,
options.action)
modifiers.append(adapter_cutter)
else:
adapter_cutter = None
if options.length_tag:
modifiers.append(LengthTagModifier(options.length_tag))
if options.strip_f3:
options.strip_suffix.append('_F3')
for suffix in options.strip_suffix:
modifiers.append(SuffixRemover(suffix))
if options.prefix or options.suffix:
modifiers.append(PrefixSuffixAdder(options.prefix, options.suffix))
if options.double_encode:
modifiers.append(DoubleEncoder())
if options.zero_cap and reader.delivers_qualities:
modifiers.append(ZeroCapper(quality_base=options.quality_base))
if options.trim_primer:
modifiers.append(PrimerTrimmer)
start_time = time.clock()
try:
if input_paired_filename:
stats = process_paired_reads(reader, modifiers, writers)
else:
stats = process_single_reads(reader, modifiers, writers)
except KeyboardInterrupt as e:
print("Interrupted", file=sys.stderr)
sys.exit(1)
except IOError as e:
if e.errno == errno.EPIPE:
sys.exit(1)
raise
except seqio.FormatError as e:
print("Error:", e, file=sys.stderr)
sys.exit(1)
# close open files
for f in [
trimmed_outfile, untrimmed_outfile, trimmed_paired_outfile,
untrimmed_paired_outfile, options.rest_file, options.wildcard_file,
options.info_file, too_short_outfile, too_long_outfile,
options.info_file, demultiplexer
]:
if f is not None and f is not sys.stdin and f is not sys.stdout:
f.close()
if not options.quiet:
# send statistics to stderr if result was sent to stdout
stat_file = sys.stderr if options.output is None else None
print_statistics(adapters,
time.clock() - start_time,
stats,
options.action,
adapter_cutter.reads_matched if adapter_cutter else 0,
options.error_rate,
too_short_filter.too_short if too_short_filter else 0,
too_long_filter.too_long if too_long_filter else 0,
cmdlineargs,
file=stat_file)
