BioPerl

That is unusual. The only recourse is to submit a bug report to Github and attach an example report giving the error. My feeling is that this might be a change in the output for FASTA. chris On Jul 24, 2014, at 12:54 PM, Antony Vincent <antony.vincent.1< at >ulaval.ca> wrote: >

You’ll have to be more explicit. What is the analysis (BLAST, FASTA, BLAT, etc)? What is the expected result? Most of the above parsers will take the hit name as the first set of non-whitespace characters, and anything after that is put into the ... [More] description. chris On Jul 24, 2014, at 12:04 PM, Antony03 <antony.vincent.1< at >ulaval.ca> wrote: [Less]

Hello, When I use hit->description I get a truncated result like this: repB putative plasmid replication protein R I tried hit->description(500) and I get the same result. Is there something wrong? Thanks -- View this message in ... [More] context: http://bioperl.996286.n3.nabble.com/length-of-hit-description-tp17596.html Sent from the Bioperl-L mailing list archive at Nabble.com. [Less]

I’ll check, it’s possible something changed when we went OpenID only (older logins used to work). chris On Jul 23, 2014, at 9:34 PM, Mark A. Jensen <maj< at >fortinbras.us> wrote:

Can someone help me connect my OpenId to my existing wiki acct? I could probably do it myself, but---hey, I can't log in! Instructions to do so at http://www.bioperl.org/wiki/OpenID are no longer valid. Thanks very much- MAJ

I’m not sure it has been officially announced, so apologies if this is a repeat post. We are moving all future bug reports and feature requests to Github. At the moment we will keep the current redmine instance with the original bug reports but we ... [More] consider it read-only; issues will possibly be migrated over time. We have made changes documenting this on the main BioPerl wiki and to the relevant code. Let us know if you have any questions or concerns. chris [Less]

Yep, that’s where to send it. I’ll post an official (belated) announcement. chris On Jul 22, 2014, at 10:38 PM, Mark A. Jensen <maj< at >fortinbras.us<mailto:maj< at >fortinbras.us>> wrote: This is a bug, and fairly deep. ... [More] I have made https://github.com/bioperl/bioperl-run/issues/12. (I hope that's what we do around here now...) cheers MAJ On 2014-07-21 15:24, Mark A Jensen wrote: Almost positive this will require a mod in SABP. I will try to have a look. MAJ On Mon, Jul 21, 2014 at 1:54 PM, Ashton Trey Belew <abelew< at >gmail.com<mailto:abelew< at >gmail.com> [1]> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Dario, Below is a portion of a little script which I use for StandAloneBlast and which uses -m 7. It doesn't exactly answer your question, but I hope it will be similar enough to prove helpful. My ignorant thought is that you can modify my use of -m to suit your purpose; but after rereading your message I am guessing you already tried something similar. -Trey my < at >params = (-program => 'blastn', [Less]

This is a bug, and fairly deep. I have made https://github.com/bioperl/bioperl-run/issues/12. (I hope that's what we do around here now...) cheers MAJ On 2014-07-21 15:24, Mark A Jensen wrote: _______________________________________________ ... [More] Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

_______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l

Hello Trey, Thanks for the answer. StandAloneBlast uses the ncbi legacy programs (blastall), while StandAloneBlastPlus uses the new NCBI blast+ programs. And -outfmt in the new programs is kind of the equivalent to -m in the old blastall. As a ... [More] matter of fact, at first I had a script that used StandAloneBlast, and adapted it to use StandAloneBlastPlus, hoping that I could make use of the new features and customize the output to include the query coverage. Now I have a script that performs exactly as the old one but using the new blast+, but I'm stuck with the output customization thing because I pass the -outfmt value between quotes, but they seem to disappear somewhere I can't figure out. Darío Carballido -----Mensaje original----- De: bioperl-l-bounces+dcarball=tandar.cnea.gov.ar< at >mailman.open-bio.org [mailto:bioperl-l-bounces+dcarball=tandar.cnea.gov.ar< at >mailman.open-bio.org] En nombre de Ashton Trey Belew Enviado el: lunes, 21 de julio de 2014 14:46 Para: bioperl-l< at >mailman.open-bio.org Asunto: Re: [Less]