x2y.py

#!/usr/bin/env python

"""
Simple script that uses Biopython SeqIO to convert
between various file formats for sequence data.

See documentation online at:
http://biopython.org/wiki/SeqIO
"""


# 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.


import traceback
import os
import sys
import warnings

__author__ = "Joe R. J. Healey"
__version__ = "1.0.0"
__title__ = "x2y"
__license__ = "GPLv3"
__author_email__ = "J.R.J.Healey@warwick.ac.uk"


def parseArgs():
	"""Parse command line arguments"""

	import argparse

	try:
		parser = argparse.ArgumentParser(
				description='Convert between sequence file types supported by BioPython')
		parser.add_argument('-i',
                	            '--infile',
                        	    action='store',
				    default='None',
                            	    help='The input sequence file to convert.')
	        parser.add_argument('-j',
                            	    '--intype',
                            	    action='store',
			    	    default='None',
                            	    help='Specify the input file type. Script will try to guess from the extension if it is standard.')
		parser.add_argument('-o',
                            	    '--outfile',
                           	    action='store',
				    default='None',
                            	    help='The output file name (default is infile with new extension.)')
		parser.add_argument('-p',
				    '--outtype',
				    action='store',
				    help='The output file type.')
		parser.add_argument('-v',
                           	    '--verbose',
                            	    action='count',
                            	    default=0,
                            	    help='Verbose behaviour, emit messages about progress/debugging etc.')
	except:
		print("An exception occurred with argument parsing. Check your provided options.")
		traceback.print_exc()

	return parser.parse_args()


def convert(infile, type, outtype, outfile):
	"""Make SeqIO call to convert using the specified parameters"""

	from Bio import SeqIO

	ifh = SeqIO.parse(infile, type)
	SeqIO.write(ifh, outfile, outtype)
	


def getOutfile(infile, outtype):
    """Synthesise a default output name if none was provided"""
    # Return an output file with the input file name and extension, but with " appended.

    return os.path.splitext(infile)[0] + "." + outtype


def guessExt(infile, verbose):
	"""If no input type was specified, guess it from the extension name or emit a warning"""
	extension = os.path.splitext(infile)[1]
	if verbose > 0: print("Extension is " + extension)
	# Figure out what extension to return
	if extension in (".abi",".ab1"):
		type = "abi"
	elif extension in (".embl"):
		type = "embl"
	elif extension in (".clust", ".cw", ".clustal"):
		type = "clustal"
	elif extension in (".fa", ".fasta", ".fas", ".fna", ".faa", ".afasta"):
		type = "fasta"
	elif extension in (".fastq", ".fq"):
		type = "fastq"
	elif extension in (".gbk", ".genbank", ".gb"):
		type = "genbank"
	elif extension in (".paup", ".nexus"):
		type = nexus
	else:
		print("Couldn't determine the file type from the extension. Reattempt with the -j|--intype option specified.")
		sys.exit(1)
	
	if verbose > 0:	print("Your file looks like a " + type)
	return type



def main():
	args = parseArgs()
		

	infile = args.infile
	type = args.intype
	outfile = args.outfile
	outtype = args.outtype
	verbose = args.verbose

        if verbose > 1: print(args)

	if type is 'None':
		type = guessExt(infile, verbose)

	if outfile is 'None':
		outfile = getOutfile(infile,outtype)

	if verbose > 0:
		print("Converting " + infile + " of type: " + type + ", to " + outfile + " of type: " + outtype)
	
	if infile is not 'None':
		convert(infile, type, outtype, outfile)
	else:
		print("No input file was provided. Check the options you provided.")
		sys.exit(1)




if __name__ == '__main__':
    main()