[Biopython] gff3 file

Atteyet-Alla.Yassin at ukb.uni-bonn.de Atteyet-Alla.Yassin at ukb.uni-bonn.de
Tue Jun 2 10:11:47 UTC 2015



I would like to convert a gff file (which I recieved on converting a
sequence in Genbank format using bioperl) in table e.g. like the following
one:

Seqname	Source		feature		Start		End
Score		Strand		Frame		Attributes
chr1		hg19_gold	exon		67088326	67183780	0,000000	+		.
	gene_id "AL139147.7"; transcript_id "AL139147.7"

In my gff file you will observe the following :

Lines are doubled i.e repeated e.g.


CP008802    Genbank    gene    417    638    .    +    .    ID=FB03_00010
CP008802    Genbank    CDS    417    638    .    +    .
Parent=FB03_00010.t00;db_xref=EnsemblGenomes-Gn%3AFB03_00010,EnsemblGenomes-Tr%3AAIE81925,UniProtKB%2FTrEMBL%3AA0A068NGQ6;codon_start=1;inference=COORDINATES%3Aab%20initio%20prediction%3AGeneMarkS%2B;product=hypothetical%20protein;translation=MAKRKKKDRGGVLTWVGIFAIVLASIADFVLFFFDNGSRYILYTLPLWFLGIGCFAWLGRAEERRNNTKRTGN;transl_table=11;note=Derived%20by%20automated%20computational%20analysis%20using%20gene%20prediction%20method%3A%20GeneMarkS%2B.;protein_id=AIE81925.1
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