getNoException.py

#! /usr/bin/env python
'''
Retrieves sequences with no annotated exceptions.
Also retrieves the longest isoform for each gene.
'''
import sys
import argparse
import gzip
#from multiprocessing import Process, current_process, freeze_support, Pool
#Multiproccessing is not necessary because the program is fast. 
#However, if it were to be implemented, the commented out lines would probably be necessary.

def parseArgs():
	'''
	Parses arguments. An input fasta file is required. 
	The number of cores is optional. By default, all available threads are used.
	An output file is optional. If an output file is not specified, output will be writted to standard out.
	'''
	import os
	parser = argparse.ArgumentParser(description='Find Orthologs in Two Files.')
	parser.add_argument("-i",help="Input FASTA file",action="store", dest="input", required=True)
	parser.add_argument("-o",help="Output FASTA File",action="store",dest="output", required=False)
	#parser.add_argument("-t",help="Number of Cores",action="store",dest="threads",type=int, default=-1, required=False)
	args = parser.parse_args()
	if not os.path.isfile(args.input):
		print args.input, "is not a correct file path!"
		sys.exit()
	return args


def writeGoodLines(args):
	'''
	Input: System arguments with input and output files
	Writes fasta sequence lines that pass the filters and are the longest isoform to the output file (or standard out)
	'''
	input = ""
	if args.input[-3:]=='.gz':
		input = gzip.open(args.input,'r')
	else:
		input = open(args.input,'r')
	output = sys.stdout
	if args.output:
		output = open(args.output,'w')
	header = ''
	geneName = ''
	countTotal = 0
	goodHeader = False
	bestGenes = dict()
	for line in input:
		line = line.strip()
		if goodHeader:
			if 'Error' in line:
				goodHeader=False
				continue
			else:
				countTotal +=1
				if geneName in bestGenes:
					if len(bestGenes[geneName][1])<len(line):
						bestGenes[geneName][0] = header
						bestGenes[geneName][1] = line
				else:
					bestGenes[geneName] = []
					bestGenes[geneName].append(header)
					bestGenes[geneName].append(line)
				header = ""
				if countTotal ==1:
					goodHeader=False
					countTotal = 0
		elif line[0] == '>':
			if 'exception' in line:
				continue
			if 'transl_except' in line:
				continue
			if 'partial=true' in line:
				continue
			if "gene=" in line:
				geneName = line.split("gene=")[1].split(";")[0]
			else:
				geneName = line
			header=line
			goodHeader = True
			countTotal = 0
	
	for key in bestGenes:
		for line in bestGenes[key]:
			output.write(line + "\n")
	input.close()
	output.close()

if __name__ =='__main__':
	'''
	Main
	'''
	#freeze_support()
	args = parseArgs()
	writeGoodLines(args)