Comments on: Short Bioinformatics Hacks: Glimmer Splitter http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/ The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Wed, 01 Feb 2012 18:43:57 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: edge http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/comment-page-1/#comment-710 edge Mon, 08 Mar 2010 03:22:56 +0000 http://bytesizebio.net/?p=2650#comment-710 <a href="#comment-589" rel="nofollow">@Andrew Perry </a> Hi Perry, Do you already successful write a script to generate GFF3 format by using GlimmerHMM output? Can I ask your opinion about the way to write the script? Thanks a lot for your sharing. 5 @Andrew Perry
Hi Perry,

Do you already successful write a script to generate GFF3 format by using GlimmerHMM output?
Can I ask your opinion about the way to write the script?
Thanks a lot for your sharing.
5

]]> By: Iddo http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/comment-page-1/#comment-591 Iddo Fri, 30 Oct 2009 12:48:16 +0000 http://bytesizebio.net/?p=2650#comment-591 <a href="#comment-589" rel="nofollow">@Andrew Perry </a> You may want to check out Brad Chapman's blog: http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/ @Andrew Perry
You may want to check out Brad Chapman’s blog:

http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/

]]> By: Peter http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/comment-page-1/#comment-590 Peter Fri, 30 Oct 2009 11:07:45 +0000 http://bytesizebio.net/?p=2650#comment-590 Hi Iddo, Nice post :) Did you know that with Biopython 1.45 or later, if the file contains *exactly* once sequence, you can do: seq_record = SeqIO.read(open(fasta_file),"fasta") instead of the more cryptic: seq_record = SeqIO.parse(open(fasta_file),"fasta").next() For the final steps of the script, since Biopython 1.50 you can slice a SeqRecord, and I've started thinking about how a SeqRecord reverse complement method might work: http://lists.open-bio.org/pipermail/biopython-dev/2009-October/006851.html Maybe you could share your thoughts on this over on the mailing list? Hi Iddo, Nice post :)

Did you know that with Biopython 1.45 or later, if the file contains *exactly* once sequence, you can do:
seq_record = SeqIO.read(open(fasta_file),”fasta”)

instead of the more cryptic:
seq_record = SeqIO.parse(open(fasta_file),”fasta”).next()

For the final steps of the script, since Biopython 1.50 you can slice a SeqRecord, and I’ve started thinking about how a SeqRecord reverse complement method might work:
http://lists.open-bio.org/pipermail/biopython-dev/2009-October/006851.html
Maybe you could share your thoughts on this over on the mailing list?

]]> By: Andrew Perry http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/comment-page-1/#comment-589 Andrew Perry Fri, 30 Oct 2009 03:08:45 +0000 http://bytesizebio.net/?p=2650#comment-589 Whoops, looks like in my excitement, I responded too soon. GlimmerHMM outputs slightly different 'predict' format (or, alternatively, GFF3 format). If I don't find a pre-written solution first, I'll probably write my script to do GFF3 exon features -> FASTA ORFs. Whoops, looks like in my excitement, I responded too soon. GlimmerHMM outputs slightly different ‘predict’ format (or, alternatively, GFF3 format). If I don’t find a pre-written solution first, I’ll probably write my script to do GFF3 exon features -> FASTA ORFs.

]]> By: Andrew Perry http://bytesizebio.net/index.php/2009/10/29/short-bioinformatics-hacks-glimmer-splitter/comment-page-1/#comment-588 Andrew Perry Fri, 30 Oct 2009 02:51:36 +0000 http://bytesizebio.net/?p=2650#comment-588 Thanks for sharing this Iddo ... your timing is perfect :) I've been meaning to run GlimmerHMM on a draft eukaryotic genome for a particular project, and have been putting it off because I needed to write a script to do this step. I'll need to modify it to concatenate together exons from the same transcript, but otherwise it should do the trick. This seemed like something that should already implemented in some software package, somewhere, and I assumed if I held off for a little while I would find it (the analysis isn't urgent, yet). I wonder what other people use when faced with converting GFF formatted 'orf' features to FASTA formatted sequences ? Thanks for sharing this Iddo … your timing is perfect :)

I’ve been meaning to run GlimmerHMM on a draft eukaryotic genome for a particular project, and have been putting it off because I needed to write a script to do this step. I’ll need to modify it to concatenate together exons from the same transcript, but otherwise it should do the trick.

This seemed like something that should already implemented in some software package, somewhere, and I assumed if I held off for a little while I would find it (the analysis isn’t urgent, yet). I wonder what other people use when faced with converting GFF formatted ‘orf’ features to FASTA formatted sequences ?

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