comparison tools/seq_length/seq_length.py @ 2:6f29bb9960ac draft

v0.0.3 - Fixed SFF; more tests

1:458f987918a6

"""

from __future__ import print_function

import sys

if "-v" in sys.argv or "--version" in sys.argv:
    print("v0.0.2")
    sys.exit(0)

try:
    from Bio import SeqIO
except ImportError:
    sys.exit("Missing required Python library Biopython.")

try:
    from Bio.SeqIO.FastaIO import SimpleFastaParser
except ImportError:
    sys.exit("Biopython tool old?, missing Bio.SeqIO.FastaIO.SimpleFastaParser")


# Parse Command Line
try:
    in_file, seq_format, out_file = sys.argv[1:]
except ValueError:
    sys.exit("Expected three arguments (input file, format, output file), "
             "got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv)))


if seq_format.startswith("fastq"):
    # We don't care about the quality score encoding, just
    # need to translate Galaxy format name into something
    # Biopython will accept:
    format = "fastq"
elif seq_format.lower() == "csfasta":
    # I have not tested with colour space FASTA
    format = "fasta"
elif seq_format.lower == "sff":
    # The masked/trimmed numbers are more interesting
    format = "sff-trim"
elif seq_format.lower() in ["fasta", "qual"]:
    format = seq_format.lower()
else:
    # TODO: Does Galaxy understand GenBank, EMBL, etc yet?
    sys.exit("Unexpected format argument: %r" % seq_format)


count = 0
total = 0
with open(out_file, "w") as out_handle:

2:6f29bb9960ac

"""

from __future__ import print_function

import sys
from optparse import OptionParser

usage = r"""Use as follows to compute all the lengths in a sequence file:

$ python seq_length.py -i example.fasta -f fasta -o lengths.tsv
"""

parser = OptionParser(usage=usage)
parser.add_option('-i', '--input', dest='input',
                  default=None, help='Input sequence filename (FASTA, FASTQ, etc)',
                  metavar="FILE")
parser.add_option('-f', '--format', dest='format',
                  default=None, help='Input sequence format (FASTA, QUAL, FASTQ, SFF)')
parser.add_option('-o', '--output', dest='output',
                  default=None, help='Output filename (tabular)',
                  metavar="FILE")
parser.add_option("-v", "--version", dest="version",
                  default=False, action="store_true",
                  help="Show version and quit")
options, args = parser.parse_args()

if options.version:
    print("v0.0.3")
    sys.exit(0)
if not options.input:
    sys.exit("Require an input filename")
if not options.format:
    sys.exit("Require the input format")
if not options.output:
    sys.exit("Require an output filename")

try:
    from Bio import SeqIO
except ImportError:
    sys.exit("Missing required Python library Biopython.")

try:
    from Bio.SeqIO.FastaIO import SimpleFastaParser
except ImportError:
    sys.exit("Biopython tool old?, missing Bio.SeqIO.FastaIO.SimpleFastaParser")

in_file = options.input
out_file = options.output

if options.format.startswith("fastq"):
    # We don't care about the quality score encoding, just
    # need to translate Galaxy format name into something
    # Biopython will accept:
    format = "fastq"
elif options.format.lower() == "csfasta":
    # I have not tested with colour space FASTA
    format = "fasta"
elif options.format.lower() == "sff":
    # The masked/trimmed numbers are more interesting
    format = "sff-trim"
elif options.format.lower() in ["fasta", "qual"]:
    format = options.format.lower()
else:
    # TODO: Does Galaxy understand GenBank, EMBL, etc yet?
    sys.exit("Unexpected format argument: %r" % options.format)


count = 0
total = 0
with open(out_file, "w") as out_handle: