format-for-cytoscape.py

#! /usr/bin/env python

"""
adds "X. to the front and ." to the end of each name in the first column if it begins with Otu
used to format network attributes file for Cytoscape so that Otu names match
assumes comma separated values and unix linebreaks

usage:
python format-for-cytoscape.py filename.csv

Copyright:

    format-for-cytoscape.py Modify OTU file for use with Cytoscape
    Copyright (C) 2016  William Brazelton

    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/>.
"""

import sys
filename = sys.argv[1]
outfilename = filename.replace('.csv','.for-cys.csv')

status = 'no'
with open(filename) as file:
	for line in file:
		columns = line.split(',')
		if 'Otu' in columns[0]:
			status = 'yes'
			newname = '"X.' + columns[0] + '."'
			with open(outfilename,'a') as outfile:
				outfile.write(newname)
				for col in columns[1:]:
					outfile.write(',' + col)
		else:
			with open(outfilename,'a') as outfile:
				outfile.write(line)

if status == 'no': print 'Nothing happened. Perhaps your input file needs to be converted to Unix linebreaks? Delete the output file and try again.'