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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Antonio Gonzalez Pena"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from os.path import split, splitext
from cogent.parse.fasta import MinimalFastaParser
from cogent import DNA
from qiime.adjust_seq_orientation import rc_fasta_file, append_rc, null_seq_desc_mapper
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Get the reverse complement of all sequences"""
script_info['script_description']="""Write the reverse complement of all seqs in seqs.fasta (-i) to seqs_rc.fasta (default, change output_fp with -o). Each sequence description line will have ' RC' appended to the end of it (default,
leave sequence description lines untouched by passing -r):"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""",""" """,""" adjust_seq_orientation.py -i seqs.fasta"""))
script_info['output_description']=""""""
script_info['required_options']=[\
options_lookup['fasta_as_primary_input']\
]
script_info['optional_options']=[\
options_lookup['output_fp'],\
make_option('-r','--retain_seq_id',action='store_true',\
help='leave seq description lines untouched'+\
' [default: append " RC" to seq description lines]')
]
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
retain_seq_id = opts.retain_seq_id
if retain_seq_id:
seq_desc_mapper = null_seq_desc_mapper
else:
seq_desc_mapper = append_rc
if not output_fp:
input_file_basename, input_file_ext = \
splitext(split(input_fasta_fp)[1])
output_fp = '%s_rc%s' % (input_file_basename,input_file_ext)
rc_fasta_file(input_fasta_fp,output_fp,seq_desc_mapper)
if __name__ == "__main__":
main()
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