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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Jens Reeder"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from qiime.parse import parse_qual_scores
from qiime.make_fastq import make_fastq_single, make_fastq_multi
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="Make FASTQ file for ERA submission from \
paired FASTA and QUAL files"
script_info['script_description']="The ERA currently requires a separate \
FASTQ file for each library, split by library id. This code takes the output \
from split_libraries.py and the corresponding QUAL files and produces \
ERA-compatible FASTQ files."
script_info['script_usage']=[]
script_info['script_usage'].append(("Example:","Take input FASTA file \
input_fasta_filepath and QUAL file input_qual_filepath: make separate file \
for each library (with the -s option: assumes that the FASTA file is the \
output of split_libraries.py or similar script):","%prog -f $PWD/seqs.fna -q \
$PWD/Fasting_Example.qual -s"))
script_info['output_description']="""Matches QUAL info to FASTA entries by id,\
and writes FASTQ output to one file or to per-library files.
The FASTQ format for each record is as follows:
@seq_id [and optional description]
seq as bases
+ [and optionally with repeat of seq_id and repeat line]
qual scores as string of chr(33+qual)
"""
script_info['required_options']=[options_lookup['input_fasta'],\
make_option('-q', '--qual', dest='qual_fps',
type='existing_filepaths',
help='names of QUAL files, comma-delimited'),
]
script_info['optional_options']=[
make_option('-o','--result_fp', default=None,
type='new_filepath', help='Path to store results '
'[default: <input_sequences_filename>.fastq]'),
make_option('-s', '--split', dest='split', action='store_true',
help='make separate file for each library [default:%default]',
default=False)
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
in_fasta = open(opts.input_fasta_fp, 'U')
quals = parse_qual_scores([open(f, 'U') for f in opts.qual_fps])
if not opts.result_fp:
opts.result_fp = opts.input_fasta_fp + '.fastq'
if opts.split:
make_fastq_multi(in_fasta, quals, opts.result_fp)
else:
make_fastq_single(in_fasta, quals, opts.result_fp)
if __name__ == "__main__":
main()
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