BioPerl

All, The master branch on github is undergoing significant changes that will break your code; in short, it is missing several modules that were removed due to our work on modularization. If you really need to grab the latest stable code, I ... [More] recommend either getting the latest CPAN release (v1.6.924, just released a month ago) or using the ‘v1.6.x’ branch on GitHub, which we have been routinely patching with fixes to the main branch. If needed we can switch the default checkout branch to ‘v1.6.x' to make things easier (so far there has been no consensus about this, so I am leaving it as is for the time being). chris On Aug 1, 2014, at 1:20 PM, Tess Cherlin <tess.cherlin< at >gmail.com<mailto:tess.cherlin< at >gmail.com>> wrote: Hi Dave, Chris, Cassandra and others, I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra. ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;" Base class package "Bio::Root::Root" is empty. (Perhaps you need to 'use' the m [Less]

Let us know if you manage to get it working, we’ll be glad to accept a patch! chris On Jul 30, 2014, at 10:25 PM, Ashton Trey Belew <abelew< at >gmail.com> wrote:

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Good evening, I was fiddling with cmsearch this evening and discovered that the current infernal parser does not play well with the new version (1.1) of infernal. I am currently hacking on the ... [More] function parse_latest() in an attempt to handle the differences in formats but have hit a bit of a wall in picking up the accessions and descriptions from the cmsearch output. In a peculiar turn of events, if parse_latest does not find the accession/description fields, it seems to repeat the PARSER: loop indefinitely, in my case repeating $self->_readline on the the 10th hit. I will keep poking at it this evening, but if anyone has made greater headway, I would love some pointers. Thank you for your time, -Trey -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFT2bcsF9UIceSIYeoRArqPAKCR4ueCEKhamjkQzwHcyXWix9hy7QCgwaIf Icd5hZI3yARPRUpkcpHtZ2U= =brNJ -----END PGP SIGNATURE----- [Less]

Dear all, apologies if you receive this multiple times. We are glad to announce that we are organising the European edition of the OBF Codefest, which will take place on September 18th and 19th at the EBI in Hinxton, UK. This is the second OBF ... [More] Codefest this year, the first was held this month in Boston just before the BOSC and ISMB conferences and in September we will have the chance to expand and carry on the work and discussions started in July in the USA. The EU Codefest will precede the Genome Informatics Conference in Cambridge, so we hope that developers attending the main conference will be also interested in joining us for a couple of days of coding and discussions on collaborative projects and new ideas. The main topics that were proposed so far are: * The OpenBio projects development (BioPerl, BioPython, BioRuby, BioJava) * Semantic web technologies for biological data (e.g. RDF, OWL) * Software deployment and bioinformatics pipelines, including CloudBiolinux, Docker and GNU GUIX * NoSQL databas [Less]

You’re right, it was the comma. Sorry! _____ 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 Mark A Jensen ... [More] Enviado el: martes, 29 de julio de 2014 0:57 Para: Darío Carballido CC: bioperl-l< at >mailman.open-bio.org Asunto: Re: [Bioperl-l] Problem with StandAloneBlastPlus Dario, looking just at the error message,I think you might be missing a comma in the list of params before -outformat. On Mon, Jul 28, 2014 at 1:15 PM, Darío Carballido <dcarball< at >tandar.cnea.gov.ar> wrote: Hello Mark, When using -method_args => [ '-outfmt' => '"7 std qcovs"' ] It worked perfectly. When using -outformat => '"7 std qcovs"' (or '7 std qcovs') I got this: Argument "outformat" isn't numeric in subtraction (-) at ./new_orthoparahomlist.pl line 180. Can't use string ("46534816") as an ARRAY ref while "strict refs" in use at /usr/local/share/perl/5.14.2/Bio/Tools/Run/StandAloneBlastPlus/Bl [Less]

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

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

Hello Mark, When using -method_args => [ '-outfmt' => '"7 std qcovs"' ] It worked perfectly. When using -outformat => '"7 std qcovs"' (or '7 std qcovs') I got this: Argument "outformat" isn't numeric in subtraction (-) at ... [More] ./new_orthoparahomlist.pl line 180. Can't use string ("46534816") as an ARRAY ref while "strict refs" in use at /usr/local/share/perl/5.14.2/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods. pm line 236. BlastMethods.pm has been updated properly (I checked before writing). Thanks for your help, 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 Mark A. Jensen Enviado el: sábado, 26 de julio de 2014 0:06 Para: bioperl-l< at >mailman.open-bio.org Asunto: Re: [Bioperl-l] Problem with StandAloneBlastPlus Ok Dario, This should be fixed in the master branch -- you need the fixes in both bioperl-live and bioperl-run. -method_args => [Less]

Awesome!! -hilmar On Wed, Jul 23, 2014 at 6:28 PM, Fields, Christopher J < cjfields< at >illinois.edu> wrote:

Ok Dario, This should be fixed in the master branch -- you need the fixes in both bioperl-live and bioperl-run. -method_args => [ '-outfmt' => '"7 std qcovs"' ] should work now, and also the standard factory argument: -outformat => ... [More] '"7 std qcovs"' (and, as it turns out -outformat => '7 std qcovs' should work. That's a longer story.) Pls try and let us know- MAJ On 2014-07-23 12:13, Fields, Christopher J wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]