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create_sub_fasta.py
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#!/usr/bin/env python
"""
extracts entries from samples based on IDs and writes them to a new file
Usage:
create_sub_fasta.py <output> [--ids] [--files] [--coverage] [--fastq]
Synopsis:
Scans FASTA or FASTQ files for headers that match at least one
ID. If a header matches an ID, the entire entry is written to
a new FASTA or FASTQ file.
Required Arguments:
output: Name of file to write matches to
--ids: One or more IDs to search for
--files: One or more FASTA or FASTQ files to search
Optional Arguments:
--coverage: Obtain coverages for the obtained FASTA or FASTQ files.
The syntax for this option is as follows:
[coverage_table] [GFF file for first input file]
[GFF file for second input file] ...
WARNING: This is a very specific usage case made for
a very specific request. It will NOT give you entry
coverage in general. For more info, see Alex Hyer.
--fastq: Specifies input files as FASTQ files [Default: FASTA]
Copyright:
create_sub_fasta.py Generate a subset FASTA file matching IDs
Copyright (C) 2016 William Brazelton, Alex Hyer
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/>.
"""
from __future__ import print_function
import argparse
from bio_utils.iterators import GFF3Reader
import re
from screed.fasta import fasta_iter
from screed.fastq import fastq_iter
import sys
__author__ = 'Alex Hyer'
__version__ = '1.0.0.1'
def append_coverages(entries, table, gff3_files):
return_entries = []
for file in gff3_files:
id_converion_dict = create_id_conversion_dict(file)
database = 'Subbio' + gff3_file.split('.')[0].split(r'/')[-1]
conversion_table = read_conversion_table(table, database)
for entry in entries:
prokka_id = entry.split('\n')[0].split('>')[-1].split(' ')[0]
if prokka_id in id_conversion_dict:
contig_id = id_conversion_dict[prokka_id]
if contig_id in conversion_table:
coverage = conversion_table[contig_id]
entry_name = entry.split('\n', 1)[0]
entry_rest = entry.split('\n', 1)[1]
entry_name = entry_name + ' ' + coverage + '\n'
new_entry = entry_name + entry_rest
return_entries.append(new_entry)
return return_entries
def create_id_conversion_dict(gff3_file):
temp_dict = {}
with open(gff3_file, 'rU') as gff3_handle:
gff_reader = GFF3Reader(gff3_handle)
for entry in gff_reader.iterate():
contig_id = entry.seqid
prokka_id = entry.attributes['ID']
if prokka_id not in temp_dict:
temp_dict[prokka_id] = contig_id
return temp_dict
def fastaq_iter(file_handle, fastq=False):
"""Yields entries from a FASTA or FASTQ file, recreates original header"""
fastaq_iterator = fasta_iter if not fastq else fastq_iter
for entry in fastaq_iterator(file_handle):
if not fastq:
entry['name'] = '{0} {1}'.format(entry['name'], \
entry['description'])
else:
entry['name'] = '{0} {1}'.format(entry['name'], \
entry['annotations'])
yield entry
def extract_ids(ids, files, fastq=False):
"""Extract entries with multiple IDs from multiple samples"""
entries = []
for file in files:
with open(file, 'rU') as in_handle:
for entry in fastaq_iter(in_handle, fastq=fastq):
for id in ids:
if len(re.findall(id, entry['name'])) == 1:
to_return = ''
if not fastq:
to_return = '>{0}\n{1}\n'.format(entry['name'],
entry['sequence'])
else:
to_return = '@{0}\n{1}\n+\n{2}\n'.format(
entry['name'],
entry['sequence'],
entry['accuracy'])
entries.append(to_return)
# Stop after first ID match
break
return entries
def read_conversion_table(conversion_table_file, database):
temp_dict = {}
with open(conversion_table_file, 'rU') as table_handle:
first_line = table_handle.readline()
databases = first_line.strip().split('\t')
if database in databases:
column_number = databases.index(database)
else:
print('{0} not in {1}. Avaialble databases are:'.format(
database, conversion_table_file))
print('\n'.join(databases[1:]))
for line in table_handle:
columns = line.strip().split('\t')
contig_id = columns[0]
coverage = columns[column_number]
if coverage != 'None':
temp_dict[contig_id] = coverage
return temp_dict
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.
RawDescriptionHelpFormatter)
parser.add_argument('output',
default=None,
nargs='?',
help='name of FASTA or FASTQ file to write')
parser.add_argument('--coverage',
default=False,
help='obtain coverage for FASTA or FASTQ entries,' \
' see help for more details')
parser.add_argument('--fastq',
default=False,
action='store_true',
help='specify input file as FASTQ file [Default: FASTA]')
parser.add_argument('--files',
default=None,
nargs='*',
help='Files to extract IDs from')
parser.add_argument('--ids', metavar='IDs',
default=None,
nargs='*',
help='IDs to extract from input files')
args = parser.parse_args()
if args.output is None:
print(__doc__)
sys.exit(0)
elif args.ids is None and args.files is None:
print('Must specify one or more IDs and one or more files.')
sys.exit(1)
else:
entries = extract_ids(args.ids, args.files, fastq=args.fastq)
if args.coverage:
print('WARNING: See help before using the coverage option')
table = args.coverage[0]
gff3_files = args.coverage[1:]
entries = append_coverages(entries, table, gff3_files)
with open(args.output, 'w') as out_handle:
for entry in entries:
out_handle.write(entry)
sys.exit(0)