bioperl-live
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bioperl
Core BioPerl 1.x code
The phyloXML produced by Bio::TreeIO does not conform to the standard. Basically, when executing a script like the one below, the "phyloXML" formatted output has elements in the wrong order:...
Recent changes at NCBI will essentially obsolesce GI in favor of accession.version. A new `idtype` parameter can be used with eutils to allow submitted and returned IDs to be accessions...
This file is in dire need of updating. I have started a Google Sheet on the committers to the repo w/ their names (as best I could glean from past...
Hello, When parsing a .gbf generated by tbl2asn, such as one that is being prepared for submission, the ACCESSION fields for each locus will be empty (not assigned by genbank...
Seeing a lot of fails on CPAN Testers involving `Bio::Root::IO` which seem related to `PerlIO::eol`: http://www.cpantesters.org/cpan/report/3a0c8940-440a-11e6-8a33-ab99f1c320fe http://www.cpantesters.org/cpan/report/709f69b2-43fd-11e6-b405-83ce5bc2a771 I am TODO'ing these for the time being but they should be looked...
Various remote server errors popping up. https://gist.github.com/cjfields/9d2a346cf05a7bc3864badcf7f2546a5
Hi there, I'm parsing a whole bunch of Genbank records to get CDS sequences, and found one weird record that messes up my pipeline. The Genbank accession is S81162. It...
Basically a ticket to evaluate whether we can set up a mechanism assessing issues with downstream applications requiring BioPerl.
NCBI will [phase out](http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/) GI sequence identifiers in Sept. 2016 (tentative date appears to be Sept. 15). I'm opening this to collect any fallout bugs from the switchover; hopefully this...
[Example](http://www.cpantesters.org/cpan/report/7b1bc52a-4c6d-11e6-8807-814d1da4c10f) It seems relegated [specifically to BSD and perl 5.8.9](http://www.cpantesters.org/distro/B/bioperl.html?grade=1&perlmat=2&patches=2&oncpan=2&distmat=3&perlver=5.8.9&osname=ALL&version=1.007000_005), so very very low priority.