#! /usr/bin/env python
# from __future__ import division # / operator performs float rather than int division
import os, sys, string, cp
import SeqIO, Seq

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

Converts a file in which each line contains [name] [sequence]
to fasta format. Name and sequence strings may be separated by 
a tab or space characters.

{{out		name of outfile. Prints to stdout by default.}}
{{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: lines2fasta.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')
		
	#read from a list of input files
	file_list = dict.value('infile_list', 'in','file')
	
	#write to stdout by default
	writeToFile = 0
	if dict.status('out'):
		outfile = dict.value('out','out','file')
	else:
		outfile = sys.stdout
		v = 0
	
	# process sequences
	for file in file_list:
		while 1:
			line = file.readline()
			if line == '' : break
			if line.strip() == '' : continue
			if line.strip()[0] == '#': continue
			
			#seqToFasta( seq, linelength = 60, degap = 0, acc=0, hea=0, begEnd=None, triplets=0, v=debugLevel, replace = {} )
			#__init__( self, name, type, seq, acc='',hea='' )
			
			splitline = line.split()
			
			#### added NH 030324 to convert katie's sequence spreadsheets
			seqname = splitline[0]
			header = splitline[1:-1]
			seqstr = splitline[-1]
			seq = Seq.Seq( name=seqname, hea=string.join(header), seq=seqstr )
			thisFasta = SeqIO.seqToFasta(seq, hea=1)
			#####
						
			#seq = Seq.Seq( splitline[0], string.join(splitline[1:],'') )
			#thisFasta = SeqIO.seqToFasta(seq)
			
			outfile.write(thisFasta)
					
	if writeToFile:
		outfile.close()
	
	
if __name__ == '__main__':
	main()