bioperl-live
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bioperl
Core BioPerl 1.x code
The documentation of the cpan page indicates that this module works only with MEME 3 and 4. Are there any plans to update the module to work with MEME version...
Not sure if this is a bug in Bio::Perl as much as place where instructions for installation should be improved. Perl was working fine on my MacBook Pro but, although...
Hi, I would like to push some updates about the methods `_gff2_string` and `_gff25_string` to remove some inconsistency related to the format specifications ([Here](https://github.com/NBISweden/GAAS/blob/master/annotation/CheatSheet/gxf.md) a review of the specifications I...
Seeing some Travis test issues centered around `SplicedSeq` and `SeqFeature::Generic`, likely due to access of remote database data. https://travis-ci.org/bioperl/bioperl-live/builds/588215892
There are multiple cpantesters reporting the following failure: ``` Can't locate object method "new" via package "Bio::Search::HSP::GenericHSP::SUPER" at /usr/home/cpan/pit/bare/conf/perl-5.14.2/.cpanplus/5.14.2/build/z3V70sjNdA/BioPerl-1.7.4/blib/lib/Bio/Search/HSP/GenericHSP.pm line 182, line 2564. # Looks like your test exited with...
BioPerl used to be relatively easy to install with v1.6.9, as the vast majority of external dependencies were merely recommended in the Build.PL script (38 recommended versus 9 required). This...
It should be ` $qpmax; and $qpmin;` right ? https://github.com/bioperl/bioperl-live/blob/7cc47700c5ee5aed5e6a32966b86628c28b6b127/lib/Bio/SearchIO/Writer/GbrowseGFF.pm#L267 https://github.com/bioperl/bioperl-live/blob/7cc47700c5ee5aed5e6a32966b86628c28b6b127/lib/Bio/SearchIO/Writer/GbrowseGFF.pm#L268 It should be ` $qmmax; and $qmmin;` right ? https://github.com/bioperl/bioperl-live/blob/7cc47700c5ee5aed5e6a32966b86628c28b6b127/lib/Bio/SearchIO/Writer/GbrowseGFF.pm#L296 https://github.com/bioperl/bioperl-live/blob/7cc47700c5ee5aed5e6a32966b86628c28b6b127/lib/Bio/SearchIO/Writer/GbrowseGFF.pm#L297
t/SeqFeature/Generic.t fails if LWP::Protocol::https is not installed: ``` ... --------------------- WARNING --------------------- MSG: In attempting to join a remote location, sequence AF032048 was not in database. Will provide padding N's....
https://ncbiinsights.ncbi.nlm.nih.gov/2018/12/03/adapting-flatfile-parsers-genbank-new-accession-formats/ "the LOCUS line, includes the “Locus Name” (usually identical to the accession number), which may now grow to as long as 20 characters." "See section 3.4.4 of the GenBank...
Since I have updated my Mac to High Sierra, I cannot index properly the fasta files. There is problem with the IDs, when you print them you don't see any...