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#!/usr/bin/env python
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@gmail.com"
__status__ = "Release"
from os.path import split, splitext
from qiime.util import parse_command_line_parameters, get_options_lookup,\
make_option, subsample_fasta
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Randomly subsample sequences from a given fasta file"""
script_info['script_description']="""Subsample the seqs.fna file, randomly select 5% of the sequences:"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""",""" """,""" subsample_fasta.py -i seqs.fasta -p 0.05"""))
script_info['output_description']=""""""
script_info['required_options']=[\
options_lookup['fasta_as_primary_input'],\
make_option('-p','--percent_subsample',action='store',type='float',\
help='Specify the percentage of sequences to subsample')
]
script_info['optional_options']=[\
options_lookup['output_fp']\
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
input_fasta_fp = opts.input_fasta_fp
output_fp = opts.output_fp
percent_subsample = opts.percent_subsample
if percent_subsample > 1 or percent_subsample <= 0:
raise ValueError,('percent_subsample must be in range of 0-1')
if not output_fp:
input_file_basename, input_file_ext = \
splitext(split(input_fasta_fp)[1])
output_fp = '%s_subsample_%3.2f%s' % (input_file_basename,
percent_subsample,input_file_ext)
subsample_fasta(input_fasta_fp, output_fp, percent_subsample)
if __name__ == "__main__":
main()
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