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

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

Writes sequences in fasta format to a file in which each name 
and sequence string are contained on a single line (names and 
sequences are tab-delimited). Useful for exporting sequences 
to excel or for sorting by name or sequence.

{{out		name of outfile. Prints to stdout by default.}}
{{degap		remove gap characters from sequences.}}
{{hea		include header line after sequence name}}
{{h			Prints documentation.}}
{{v			verbosity 
	1}}
{{version   print version info and exit}}

%(version)s
"""
	debug = 0
	
	docstringdict = {'filename':os.path.split(sys.argv[0])[-1],
	'version':'$Id: fasta2lines.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')
	header = dict.status('hea')
	
	degap = dict.status('degap')
		
	#read from a list of fasta files
	fasta_list = dict.value('infile_list', 'in','file')
	fasta = SeqIO.readFastaList(fasta_list, output='list', degap=degap)

	#write to stdout by default
	writeToFile = 0
	if dict.status('out'):
		outfile = dict.value('out','out','file')
	else:
		outfile = sys.stdout
		v = 0

	for seq in fasta:
		if header:
			lineout = '%s\t%s\t%s\n' % (seq.getName(), seq.getHea(), seq.getSeq())
		else:
			lineout = '%s\t%s\n' % (seq.getName(), seq.getSeq())
		outfile.write(lineout)		
	
	
	
if __name__ == '__main__':
	main()