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

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

Reads names in a tfa file. Prints to stdout by default.

{{h			Prints documentation.}}
{{out		name of outfile}}
{{len		include length of sequence after name}}
{{c			force upper or lower case output
	u
	l}}
{{fname		include filename. Only works if a single file is used as input.}}
{{version   print version info and exit}}

%(version)s
"""
	debug = 0
	
	docstringdict = {'filename':os.path.split(sys.argv[0])[-1],
	'version':'$Id: fastanames.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 )
	printLen = dict.status('len')
	
	forceCase = 0
	if dict.status('c'):
		forceCase = 1
		if dict.value('c') == 'u': 
			casefun = string.upper
		elif dict.value('c') == 'l': 
			casefun = string.lower
	
	#read from a list of fasta files
	fasta_list = dict.value('infile_list', 'in','file')
	fasta = SeqIO.readFastaList(fasta_list, output='list')
	
	if dict.status('out'):
		outfile = dict.value('out','out','file')
	outfile = sys.stdout
	
	writename = 0
	if dict.status('fname') and len(fasta_list) == 1 and fasta_list[0].name != '<stdin>':
		writename = fasta_list[0].name
	
	
	for seq in fasta:
		outStr = seq.getName()
		if printLen:
			outStr += '\t' + `len(seq)`
		if writename:
			outStr = writename + '\t' + outStr
		if forceCase:
			outStr = casefun(outStr)
		outfile.write(outStr + '\n')

main()