[Biopython] parsing gff3 sequence

[Michiel de Hoon]

You can also consider using pybedtools to parse GFF files.
,
-Michiel.

--------------------------------------------
On Mon, 6/1/15, Peter Cock <p.j.a.cock at googlemail.com> wrote:

 Subject: Re: [Biopython] parsing gff3 sequence
 To: Atteyet-Alla.Yassin at ukb.uni-bonn.de
 Cc: "Biopython Mailing List" <Biopython at mailman.open-bio.org>
 Date: Monday, June 1, 2015, 6:59 PM
 
 Hello,
 
 Biopython can read GenBank
 files directly (e.g. using Bio.SeqIO).
 Brad
 Chapman has some GFF parsing code which integrates
 into Biopython: http://biopython.org/wiki/GFF_Parsing
 
 Biopython can be used to draw
 simple chromosome diagrams, e.g.
 http://news.open-bio.org/news/2011/10/chromosome-diagrams-in-biopython/
 
 However, you're interested
 in circos rather than Biopython.
 Could you
 clarify your question please?
 
 Peter
 
 On Sat,
 May 30, 2015 at 12:55 PM,  <Atteyet-Alla.Yassin at ukb.uni-bonn.de>
 wrote:
 > I obtained the attached gff3
 file using bioperl from a Genbank format and
 > want to use it to build chromosome map
 with circos. I have no experience
 > with
 biopython and want to know: the steps to parse it and the
 linux command
 > which should I use?
 >
 > (See attached file:
 bac.gff)
 >
 >
 >
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