bioperl-live
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bioperl
Core BioPerl 1.x code
Hi, the nexus syntax output from Bio::AlignIO::nexus is at odds with current nexus standards. For example, the BioPerl module writes ``` format interleave datatype=dna gap=- symbols="CTANG"; ``` but the software...
We have `$Bio::Root::Version::VERSION` but that seems to not be good enough to some modules that have their own indepdendent VERSION. These are: * Bio/Root/Root.pm * Bio/Root/Build.pm * BioPerl.pm which just...
There are groups of modules that have groups of equal tests. For example, `t/RemoteDB/SeqRead_fail.t` has the same test units for a series of `Bio::DB` classes. Now that those classes are...
``` Possible precedence issue with control flow operator at bin/bp_genbank2gff3 line 690 ```
More details on issue #281 but basically, there's no option to have the constructor of this classes create a new file. If the filepath points to an existing file, it...
The Bioperl mailing lists (as well as all other OBF mail lists) had been having serious issues over the last several months due to heavy spam traffic on the OBF...
The following fix was applied to 1.7 releases to deal with NNN mapping to a stop codon. https://github.com/bioperl/bioperl-live/commit/260ebb98281ce5580c9c1b9808d3167688c7626c Ensembl also encounters unexpected behaviour around the handling of start codons, where...
Do people run 'prove -w t/*' frequently or do you rely only on travis? These tests fail before and after my commits today and yesterday. This is perl 5, version...
The Bio::Species module still has memory leak problem. Can it be solved completely? And the host of bioperl is now http://bioperl.org/, not http://bioperl.open-bio.org/ any more.
Besides issue #234 , there is another problem with Bio::TreeIO. When parsing a Newick formatted file in which the internal node names are bootstrap support values, and the attempting to...
