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#!/usr/bin/env python
# File created on 08 Jan 2010.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from cogent.parse.fasta import MinimalFastaParser
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from qiime.util import extract_seqs_by_sample_id
from qiime.parse import parse_mapping_file
from qiime.filter_by_metadata import (parse_metadata_state_descriptions,
get_sample_ids)
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Extract sequences based on the SampleID"""
script_info['script_description']="""This script creates a fasta file which will contain only sequences that ARE associated with a set of sample IDs, OR all sequences that are NOT associated with a set of sample IDs (-n)"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Examples:""","""Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids S2, S3, \
S4 (-s). As always, sample IDs are case-sensitive:""","""extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs.fasta -s S2,S3,S4"""))
script_info['script_usage'].append(("""""","""Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE NOT (-n) associated with sample ids S2, S3, S4 (-s). As always, sample IDs are case-sensitive:""","""extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs.fasta -s S2,S3,S4 -n"""))
script_info['script_usage'].append(("""""","""Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids whose "Treatment" value is "Fast" in the mapping file:""","""extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs.fasta -m map.txt -s "Treatment:Fast" """))
script_info['output_description']="""The script produces a fasta file containing containing only the specified SampleIDs."""
script_info['required_options']=[
options_lookup['fasta_as_primary_input'],
make_option('-o','--output_fasta_fp',help='the output fasta file')
]
script_info['optional_options']=[
make_option('-n','--negate',action='store_true',default=False,
help='negate the sample ID list (i.e., output sample '+
'ids not passed via -s) [default: %default]'),
make_option('-s','--sample_ids',\
help="comma-separated sample_ids to include in output fasta file"+\
" (or exclude if --negate), or string describing mapping file states"+\
" defining sample ids (mapping_fp must be provided for the latter)"),
options_lookup['mapping_fp']]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
negate = opts.negate
sample_ids = opts.sample_ids
mapping_fp = opts.mapping_fp
input_fasta_fp = opts.input_fasta_fp
output_fasta_fp = opts.output_fasta_fp
if not mapping_fp:
sample_ids = sample_ids.split(',')
else:
map_data, map_header, map_comments = parse_mapping_file(mapping_fp)
sample_ids = get_sample_ids(
map_data,
map_header,
parse_metadata_state_descriptions(sample_ids))
if len(sample_ids) == 0:
raise ValueError,\
"No samples match the search criteria: %s" % valid_states
if opts.verbose:
# This is useful when using the --valid_states feature so you can
# find out if a search query didn't work as you expected before a
# lot of time is spent
print "Extracting samples: %s" % ', '.join(sample_ids)
try:
seqs = MinimalFastaParser(open(input_fasta_fp))
except IOError:
option_parser.error('Cannot open %s. Does it exist? Do you have read access?'%\
input_fasta_fp)
exit(1)
try:
output_fasta_f = open(output_fasta_fp,'w')
except IOError:
option_parser.error("Cannot open %s. Does path exist? Do you have write access?" %\
output_fasta_fp)
exit(1)
for r in extract_seqs_by_sample_id(seqs,sample_ids,negate):
output_fasta_f.write('>%s\n%s\n' % r)
output_fasta_f.close()
if __name__ == "__main__":
main()
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