BioPerl

Vandana, Bio::Structure::IO::pdb reads and writes PDB format, but Bio::Structure::SecStr::DSSP::Res only reads *dssp files. I don’t think this conversion is possible with BioPerl. Brian O. On Aug 30, 2014, at 11:08 PM, vandana Baranwal <lovevandu08< at >gmail.com> wrote:

Hello Is is possible to convert a pdb file int dssp file using bioperl. I searched a lot but didn't get a fruitful answer. I want to convert approximately 1000 pdb files into dssp files. Any help will be highly appreciated

> Just a quick update on this: I released a separate Bio::FeatureIO > release to CPAN that represents the code split out from the core > modules: > > https://metacpan.org/pod/Bio::FeatureIO > > I had to do some ... [More] cleanup to get code to work and tests passing with > some sanity. A *lot* of things were not passing tests when we > moved this over. > > This should represent what was last working with Chado though. > However, I haven’t officially announced anything yet b/c I would > like to shake bugs out of it. Can either of you try this out on a > Chado run to make sure everything is up to snuff (or at least point > out issues)? Time depending, I would like to get something running > on (for instance) Travis-CI, maybe including some optional > Chado-related stuff. This would also help so that we can work on > merging what has been done on master so that these pass the same > tests. I can't do anything until Tuesday, but will be happy to run it through the standard Chado build pro [Less]

Just a quick update on this: I released a separate Bio::FeatureIO release to CPAN that represents the code split out from the core modules: https://metacpan.org/pod/Bio::FeatureIO I had to do some cleanup to get code to work and tests passing ... [More] with some sanity. A *lot* of things were not passing tests when we moved this over. This should represent what was last working with Chado though. However, I haven’t officially announced anything yet b/c I would like to shake bugs out of it. Can either of you try this out on a Chado run to make sure everything is up to snuff (or at least point out issues)? Time depending, I would like to get something running on (for instance) Travis-CI, maybe including some optional Chado-related stuff. This would also help so that we can work on merging what has been done on master so that these pass the same tests. chris On Jul 25, 2014, at 2:59 PM, Fields, Christopher J <cjfields< at >illinois.edu<mailto:cjfields< at >illinois.edu>> wrote: The commit history is all there I beli [Less]

Seems fine; it’s essentially a convenience method that shouldn’t affect the API. chris On Aug 28, 2014, at 9:21 AM, Brian Osborne <bosborne11< at >verizon.net> wrote:

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All, Some SeqFeature modules (e.g. SeqFeature::Computation) allow things like this: my < at >sourcefeats = $seq->remove_SeqFeatures(‘source’) my < at >sourcefeats = $seq->get_SeqFeatures(‘source’) SeqFeature::Generic can’t do this. Any objection to my adding this capability to Generic? Thanks again, Brian O. —

That's a great thought. For my next trick, I was planning ot think about https://github.com/bioperl/bioperl-run/issues/11 - how to deal with dependencies within BioPerl given the splits. I can include setting up travis to test in these thoughts ... [More] (and perhaps actions)-- unless someone else is already working on this... MAJ On 2014-08-26 00:27, 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]

\o/ Not sure but we should probably set up Travis-CI tests for bioperl-run; lots of apps available via apt. -c On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <maj< at >fortinbras.us> wrote:

WrapperBase and friends removed from bioperl-live; Travis built successfully at #486. MAJ On 2014-08-25 22:08, Mark A. Jensen wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l