'quality strings on a single TAB-separated line to stdout.'))
parser.add_argument('--separator',
default='\t',
help=('The character string to separate ids from '
'sequences and quality strings (if any)'))
parser.add_argument('--removeIds',
default=False,
action='store_true',
help='Do not print sequence ids')
addFASTACommandLineOptions(parser)
args = parser.parse_args()
sep = args.separator
reads = parseFASTACommandLineOptions(args)
# Duplicate code a little so as not to repeatedly do two tests per read.
if args.fastq:
if args.removeIds:
for read in reads:
print(read.sequence + sep + read.quality)
else:
for read in reads:
print(read.id + sep + read.sequence + sep + read.quality)
else:
if args.removeIds:
for read in reads:
print(read.sequence)
else:
for read in reads:
'be ignored. The sites must be given in the form e.g., '
'24,100-200,260.'))
parser.add_argument(
'--showDiffs',
default=False,
action='store_true',
help='Print (1-based) sites where the sequence nucleotides differ.')
addFASTACommandLineOptions(parser)
args = parser.parse_args()
keepSequences = set([args.index1 - 1, args.index2 - 1])
reads = list(
parseFASTACommandLineOptions(args).filter(keepSequences=keepSequences))
if len(reads) == 1:
if len(keepSequences) == 1:
# This is ok, they want to compare a sequence with itself.
reads = Reads([reads[0], reads[0]])
else:
print('Could not find both requested sequence indices. Exiting.')
sys.exit(1)
elif len(reads) != 2:
print('Could not find both requested sequence indices. Exiting.')
sys.exit(1)
if args.alignmentFile:
args.align = True
parser = argparse.ArgumentParser(
description=(
'Given FASTA on stdin, write the ids, sequences, and '
'quality strings on a single TAB-separated line to stdout.'))
parser.add_argument('--separator', default='\t',
help=('The character string to separate ids from '
'sequences and quality strings (if any)'))
parser.add_argument('--removeIds', default=False, action='store_true',
help='Do not print sequence ids')
addFASTACommandLineOptions(parser)
args = parser.parse_args()
sep = args.separator
reads = parseFASTACommandLineOptions(args)
# Duplicate code a little so as not to repeatedly do two tests for read.
if args.fastq:
if args.removeIds:
for read in reads:
print(read.sequence + sep + read.quality)
else:
for read in reads:
print(read.id + sep + read.sequence + sep + read.quality)
else:
if args.removeIds:
for read in reads:
print(read.sequence)
else:
for read in reads:
parser.add_argument('--force',
default=False,
action='store_true',
help='If given, overwrite pre-existing files.')
parser.add_argument(
'--saveAs',
choices=('fasta', 'fastq', 'fasta-ss'),
help=('The output format. The default is to match the input format, '
'so there is usually no need to specify this option. It can be '
'used to force conversion from FASTQ to FASTA'))
addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTACommandLineOptions(args)
if not exists(args.outDir):
mkdir(args.outDir)
saveAs = (args.saveAs or (args.fasta and 'fasta') or (args.fastq and 'fastq')
or (args.fasta_ss and 'fasta-ss'))
# Note: we may be reading the FASTA input from stdin, so we cannot read it
# more than once (and I don't want to store it all because it may be very
# large). That's why we do a second phase of processing to renumber the
# files we created if --numeric is used (and --noLeadingZeroes is not).
count = 0
for count, read in enumerate(parseFASTACommandLineOptions(args), start=1):
id_ = read.id.split()[0]
parser.add_argument(
'--checkResultCount', type=int,
help=('The number of reads expected in the output. If this number is '
'not seen, the script exits with status 1 and an error '
'message is printed unless --quiet was used.'))
addFASTACommandLineOptions(parser)
addFASTAFilteringCommandLineOptions(parser)
addFASTAEditingCommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTAEditingCommandLineOptions(
args, parseFASTAFilteringCommandLineOptions(
args, parseFASTACommandLineOptions(args)))
saveAs = (
args.saveAs or
(args.fasta and 'fasta') or
(args.fastq and 'fastq') or
(args.fasta_ss and 'fasta-ss'))
# Check for incompatible read/write formats. We can't write FASTQ
# unless we have FASTQ on input (else we won't have quality information),
# and we can't write PDB FASTA with secondary structure information
# unless we have that on input.
if saveAs == 'fastq' and not args.fastq:
raise ValueError(
'You have specified --saveAs fastq without using --fastq '
'to indicate that the input is FASTQ. Please be explicit.')
'start of this sequence will be counted and offsets will be '
'incremented by that amount (and lower offsets in sequences '
'that start before the specified sequence will be ignored).'))
parser.add_argument(
'--unknownAreAmbiguous',
action='store_true',
default=False,
help=("Any unknown character (e.g., a '-' gap or '?' unknown base) "
"will be treated as being fully ambiguous (i.e., could be any "
"of ACGT). Otherwise, all unknown characters are counted "
"as '-' characters."))
addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = Reads(list(parseFASTACommandLineOptions(args)))
if not reads:
sys.exit(0)
if args.reference:
for read in reads:
if read.id == args.reference:
break
else:
print('Could not find --reference sequence %r.' % args.reference,
file=sys.stderr)
sys.exit(1)
baseOffset = len(read.sequence) - len(read.sequence.lstrip('-'))
reference = read
else:
parser.add_argument(
'--sites',
help=('Specify (1-based) sequence sites to keep. All other sites will '
'be ignored. The sites must be given in the form e.g., '
'24,100-200,260.'))
parser.add_argument(
'--showDiffs', default=False, action='store_true',
help='Print (1-based) sites where the sequence nucleotides differ.')
addFASTACommandLineOptions(parser)
args = parser.parse_args()
keepSequences = set([args.index1 - 1, args.index2 - 1])
reads = list(parseFASTACommandLineOptions(args).filter(
keepSequences=keepSequences))
if len(reads) == 1:
if len(keepSequences) == 1:
# This is ok, they want to compare a sequence with itself.
reads = Reads([reads[0], reads[0]])
else:
print('Could not find both requested sequence indices. Exiting.')
sys.exit(1)
elif len(reads) != 2:
print('Could not find both requested sequence indices. Exiting.')
sys.exit(1)
if args.alignmentFile:
args.align = True
'--noLeadingZeroes', default=False, action='store_true',
help='If given, numeric filenames will not have leading zeroes.')
parser.add_argument(
'--force', default=False, action='store_true',
help='If given, overwrite pre-existing files.')
parser.add_argument(
'--saveAs', choices=('fasta', 'fastq', 'fasta-ss'),
help=('The output format. The default is to match the input format, '
'so there is usually no need to specify this option. It can be '
'used to force conversion from FASTQ to FASTA'))
addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTACommandLineOptions(args)
if not exists(args.outDir):
mkdir(args.outDir)
saveAs = (
args.saveAs or
(args.fasta and 'fasta') or
(args.fastq and 'fastq') or
(args.fasta_ss and 'fasta-ss'))
# Note: we may be reading the FASTA input from stdin, so we cannot read it
# more than once (and I don't want to store it all because it may be very
# large). That's why we do a second phase of processing to renumber the
# files we created if --numeric is used (and --noLeadingZeroes is not).
help='If given, numeric filenames will not have leading zeroes.')
parser.add_argument('--force',
action='store_true',
help='If given, overwrite pre-existing files.')
parser.add_argument(
'--saveAs',
choices=('fasta', 'fastq', 'fasta-ss'),
help=('The output format. The default is to match the input format, '
'so there is usually no need to specify this option. It can be '
'used to force conversion from FASTQ to FASTA'))
addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTACommandLineOptions(args)
if not exists(args.outDir):
mkdir(args.outDir)
saveAs = (args.saveAs or (args.fasta and 'fasta') or (args.fastq and 'fastq')
or (args.fasta_ss and 'fasta-ss'))
# Note: we may be reading the FASTA input from stdin, so we cannot read it
# more than once (and I don't want to store it all because it may be very
# large). That's why we do a second phase of processing to renumber the
# files we created (if --noLeadingZeroes is not used).
outDir = Path(args.outDir)
count = 0
'--checkResultCount',
type=int,
help=('The number of reads expected in the output. If this number is '
'not seen, the script exits with status 1 and an error '
'message is printed unless --quiet was used.'))
addFASTACommandLineOptions(parser)
addFASTAFilteringCommandLineOptions(parser)
addFASTAEditingCommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTAEditingCommandLineOptions(
args,
parseFASTAFilteringCommandLineOptions(
args, parseFASTACommandLineOptions(args)))
saveAs = (args.saveAs or (args.fasta and 'fasta')
or (args.fastq and 'fastq') or (args.fasta_ss and 'fasta-ss'))
# Check for incompatible read/write formats. We can't write FASTQ
# unless we have FASTQ on input (else we won't have quality information),
# and we can't write PDB FASTA with secondary structure information
# unless we have that on input.
if saveAs == 'fastq' and not args.fastq:
raise ValueError(
'You have specified --saveAs fastq without using --fastq '
'to indicate that the input is FASTQ. Please be explicit.')
elif saveAs == 'fasta-ss' and not args.fasta_ss:
raise ValueError(
'You have specified --saveAs fasta-ss without using --fasta-ss '
