[Biojava-l] Issue with FASTA reader

[Rojnuckarin, Dak]

Hi,

I am trying to commit my branch and got “git-receive-pack not permitted”. I suspect I need commit privilege for biojava repository. If so, my github username is arojnuckarin (email: atipatr at amgen.com<mailto:atipatr at amgen.com>). If not, I would appreciate any help figuring this out.

Thanks,
dak

From: Jose Duarte [mailto:jose.duarte at rcsb.org]
Sent: Thursday, June 1, 2017 10:37 AM
To: Rojnuckarin, Dak <atipatr at amgen.com>
Cc: Andreas Prlic <andreas at sdsc.edu>; biojava-l at mailman.open-bio.org
Subject: Re: [Biojava-l] Issue with FASTA reader

Dear Dak

The best way of fixing it yourself is that you modify the code in your own github fork (ideally in a branch, not in master) and then submit a pull request so that your patch can be peer reviewed.

All the best

Jose


On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <atipatr at amgen.com<mailto:atipatr at amgen.com>> wrote:
Hello,

Andreas mentioned he created a branch in github to contain my test code:

https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e21684605cf2f7b

but I have not heard back in a while.

What’s the process/etiquette of getting involved and attempt the fix myself?

Thanks,
dak

From: andreas.prlic at gmail.com<mailto:andreas.prlic at gmail.com> [mailto:andreas.prlic at gmail.com<mailto:andreas.prlic at gmail.com>] On Behalf Of Andreas Prlic
Sent: Wednesday, April 19, 2017 4:34 PM
To: Rojnuckarin, Dak <atipatr at amgen.com<mailto:atipatr at amgen.com>>
Cc: biojava-l at mailman.open-bio.org<mailto:biojava-l at mailman.open-bio.org>
Subject: Re: [Biojava-l] Issue with FASTA reader

Thanks, Dak. I'll create a branch in git which will contain your test, then we can take it from there.

Andreas



On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <atipatr at amgen.com<mailto:atipatr at amgen.com>> wrote:
Hi,

I have a FASTA file that contain one sequence. I initialized FASTA reader as described in the tutorial, called process() and get one record as expected. However, if I re-initialized another FASTA reader opening the same one-record file, called process(1) and null is returned. If I tried to read two-record FASTA file, the first process(1) works, but not the second call to process(1) return null. Based on a superficial glance, it looks like the if statement at line 194 of FastaReader.java may be the culprit.

Test code attached.

Thanks,
Dak Rojnuckarin
Research Informatics
Amgen



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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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