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#!/usr/bin/env python3
#
# Copyright (C) 2010 Institute for Computational Biomedicine,
# Weill Medical College of Cornell University
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import getopt
import struct
import sys
import textwrap
from goby.Reads import CompactReads, decodeSequence
def usage():
print("usage:", sys.argv[0],
"[-h|--help] [-v|--verbose] [-f|--format <fasta|fastq>] [-o|--output <output-filename>] <filename>")
def main():
verbose = False
format = "fasta"
output = sys.stdout
fake_quality_score = 40
try:
opts, args = getopt.getopt(sys.argv[1:], "f:o:hv", ["format=", "output=", "help", "verbose"])
except getopt.GetoptError as err:
print( str(err), file=sys.stderr)
usage()
sys.exit(1)
# Collect options
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt in ("-v", "--verbose"):
verbose = True
elif opt in ("-f", "--format"):
format = arg
elif opt in ("-o", "--output"):
output = open(arg, "w")
if format != "fasta" and format != "fastq":
print( "Format", format, "is not supported", file=sys.stderr)
usage()
sys.exit(3)
if len(args) != 1:
usage()
sys.exit(2)
filename = args[0]
if verbose:
print("Processing file =", filename)
if format == "fasta":
new_entry_character = ">"
else:
new_entry_character = "@"
for entry in CompactReads(filename):
# if the entry has a description, use it otherwise use the index
if (entry.HasField("description")):
description = entry.description
else:
description = entry.read_index
print ("%c%s" % (new_entry_character, description), file=output)
for line in textwrap.wrap(text=decodeSequence(entry.sequence), width=60):
print( line, file=output)
if format == "fastq":
print("+", file=output)
quality_string = ""
if entry.HasField("qualityScores"):
for quality_score in entry.quality_scores:
quality_string += chr(struct.unpack("B", quality_score)[0] + 64) # Assume Illumina encoding
else:
# fill the string with a constant quality code
quality_string = quality_string.ljust(len(entry.sequence), chr(fake_quality_score + 64))
for line in textwrap.wrap(quality_string, 60):
print( line, file=output)
if __name__ == "__main__":
main()
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