#! /usr/bin/env python
import os, sys, string, cp
import SeqIO

def main():
	"""
%(filename)s

Converts an alignment in selex format to fasta format. Selex is the 
default output format used by hmmer. 

{{degap		remove gaps}}

{{h			Prints documentation.}}
{{v			verbosity 
	1}}
{{out		name of outfile}}
{{version   print version info and exit}}

%(version)s
"""
	debug = 0
	
	docstringdict = {'filename':os.path.split(sys.argv[0])[-1],
	'version':'$Id: selex2fasta.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $'}
	
	optlist, formattedDocString, formattedSummary = cp.optStringParser(main.__doc__ % docstringdict,
		optWidth=15, lineWidth=60, valOffset = 4, putVals=1)	
	dict = cp.commandparser(options=optlist, usage='Options:\n' + formattedSummary, 
		debug = debug, exitWithUsage=1)
		
	if dict.status('version'):
		sys.exit( 'Version: %(version)s\n' % docstringdict )
		
	if dict.status('h'):
		print formattedDocString
		sys.exit( 0 )
	v = dict.value('v')
	
	degap = dict.status('degap')
	
	#write to stdout by default
	writeToFile = 0
	if dict.status('out'):
		outfile = dict.value('out','out','file')
	else:
		outfile = sys.stdout
		v = 0
		
	infile = dict.value('infile','in','file')
	
	seqList = SeqIO.readSelex( infile )
	
	#seqToFasta( seq, linelength = 60, degap = 0, acc=0, hea=0, begEnd=None, triplets=0, v=debugLevel, replace = {} )
	if v>0:
		print 'Writing', outfile.name
	
	for seq in seqList:
		outfile.write( SeqIO.seqToFasta(seq, degap=degap) )
	
	if writeToFile:
		outfile.close()
	
if __name__ == '__main__':
	main()