Parse the castaneum gff file to extract all genes with multiple exons. I'd like to make this robust at some point to repeat this process with any genome gff3 file however in the interest of finishing this project and getting it written up this semester the current version is only tested on the castaneum genome (version 3) gff3 file.

retro-gff3parser.py

# the gff3 file that was used as input for this script was downloaded from:
# ftp://ftp.ensemblgenomes.org/pub/metazoa/release-21/gff3/tribolium_castaneum
# on January 10, 2014

import re
## This script is just to parse out the part of the gff file that we
## are interested in, (i.e. lines describing exons or protein coding genes


## Here we specify the name of the gff3 
## file that we would like to parse
        #I would like to have the command line allow you to enter a file name
        #DataIn = input('Enter your file name: ')     
        #right now you have to quote your file name?
DataIn = "./chromosomes/t.cast.gff3"
gff = open(DataIn)
lines = gff.readlines()


## now we create a list of multiple exon genes
## the variable exonLines will hold all lines 
## with the feature name exon
exonLines = []
for i in range(0, len(lines)):
	foo = lines[i].split()    
	tempLines = []      
	if len(foo) > 2 and foo[2] == 'exon':
		tempLines.append(foo[0])
		tempLines.append(foo[3])
		tempLines.append(foo[4])
		bar = foo[8].split(':')
		tempLines.append(bar[1][0:8])
		exonLines.append(tempLines) 
		
		
## now we just want to create a list of TC numbers
## we will use this to get a list of all TCs that 
## have more than a single exon		
tcList = []
for i in range(0, len(exonLines)):
	tcList.append(exonLines[i][3])
from collections import Counter
foo = Counter(tcList)
dictTC = {k:v for (k,v) in foo.items() if v > 1}  # this is the line that pulls the > 1 exons
multiexon = list(dictTC)

## now lets create a final list that has just the info
## we care about for the multi exon genes
multiExonLines = []
for i in range(0, len(exonLines)):
	if exonLines[i][3] in multiexon:
		multiExonLines.append(exonLines[i])

print multiExonLines[1]
print multiExonLines[2]


import csv
with open('exons.csv', 'wb') as f:
	wr = csv.writer(f)
	wr.writerow(multiExonLines)