gff-parser's Introduction

GFF-Parser

A python GFF parser.

General Feature Format (GFF) also known as Gene-Finding Format is a file format which describes the features of genomic and protein sequences. A GFF file is a tab delimited text file where each feature is described on a single line.

More information about GFF format can be found at Wellcome Trust Sanger Institute.

e.g. for maize, the GFF file I used looks like -

9	ensembl	chromosome	1	156750706	.	.	.	ID=9;Name=chromosome:AGPv2:9:1:156750706:1
9	ensembl	gene	66347	68582	.	-	.	ID=GRMZM2G354611;Name=GRMZM2G354611;biotype=protein_coding
9	ensembl	mRNA	66347	68582	.	-	.	ID=GRMZM2G354611_T01;Parent=GRMZM2G354611;Name=GRMZM2G354611_T01;biotype=protein_coding
9	ensembl	intron	68433	68561	.	-	.	Parent=GRMZM2G354611_T01;Name=intron.1

Usage:

from gff import gffParser
import sys
    
input_file = sys.argv[1]
out = gffParser(input_file)

## get genes in the chromosome 1
out.getGenes("1")

## get mRNA corresponding to a gene
out.getmRNA(chrom, gene)

## get coding regions in the mRNA
out.getCDS(chrom, mRNA)

## get introns/exons
out.getInrons(chrom, mRNA)
out.getExonss(chrom, mRNA)

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IndexError: list index out of range

Hey there,

I'm trying to parse my gff3 file.

File "gff_1.py", line 5, in
out = gffParser(input_file)
File "/myscratch/GFF-Parser/gff.py", line 35, in init
source = record[1]
IndexError: list index out of range

I keep getting this error, could you please help me?

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