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

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

Calculates the consensus for an alignment of nucleotide or protein sequences.

{{cg		include to count gaps in the consensus calculation}}
{{plu		plurality required for assignment of consensus to a character
	2}}
{{h			Prints documentation.}}
{{v			verbosity 
	1}}
{{out		name of outfile. Writes to stdout if unspecified.}}
	
{{version   print version info and exit}}

%(version)s
"""
	debug = 0
	
	docstringdict = {'filename':os.path.split(sys.argv[0])[-1],
	'version':'$Id: consensus.py,v 1.1 2004/10/10 02:53:09 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')
	
	countgaps = dict.status('cg')
	plurality = dict.value('plu')
		
	#read from a list of fasta files
	fasta_list = dict.value('infile_list', 'in','file')
	fasta = SeqIO.readFastaList(fasta_list, output='list')
	
	#write to stdout by default
	writeToFile = 0
	if dict.status('out'):
		outfile = dict.value('out','out','file')
	else:
		outfile = sys.stdout
		v = 0
		
	if len(dict.value('infile_list')) == 1 and dict.value('infile_list')[0] != '<stdin>':
		name = os.path.splitext(dict.value('infile_list')[0])[0] + '_cons'
	else:
		name = 'consensus'

	# tabulate list of sequence objects
	# tabulate( seqList, v=debugLevel )
	tab = SeqIO.tabulate( fasta )
	
	# consensus( dict, countGaps=0, plu=2, v=debugLevel )
	consStr = ''
	for pos in tab:
		consStr += SeqIO.consensus( pos, countGaps=countgaps, plu=plurality, v=0 )
	
	outfile.write( SeqIO.seqToFasta(Seq.Seq(name=name, seq=consStr)) )
	
	
if __name__ == '__main__':
	main()