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#!/usr/bin/env python
# File created on 20 Oct 2011
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,
make_option,
split_fasta_on_sample_ids_to_files)
script_info = {}
script_info['brief_description'] = "Split a single post-split_libraries.py fasta file into per-sample fasta files."
script_info['script_description'] = "Split a single post-split_libraries.py fasta file into per-sample fasta files. This script requires that the sequences identitifers are in post-split_libraries.py format (i.e., SampleID_SeqID). A fasta file will be created for each unique SampleID."
script_info['script_usage'] = [("","Split seqs.fna into one fasta file per sample and store the resulting fasta files in 'out'","split_fasta_on_sample_ids.py -i seqs.fna -o out/")]
script_info['output_description']= ""
script_info['required_options'] = [
make_option('-i','--input_fasta_fp',type="existing_filepath",help='the input fasta file to split'),
make_option('-o','--output_dir',type="new_dirpath",help='the output directory [default: %default]'),\
]
script_info['optional_options'] = [\
make_option('--buffer_size',type="int",default=500,
help="the number of sequences to read into memory before writing to file (you usually won't need to change this) [default: %default]"),\
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
split_fasta_on_sample_ids_to_files(MinimalFastaParser(open(opts.input_fasta_fp,'U')),
opts.output_dir,
opts.buffer_size)
if __name__ == "__main__":
main()
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