bioperl-live
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bioperl
Core BioPerl 1.x code
This warning has shown up for years -- https://github.com/bioperl/bioperl-live/blob/2b53e22cd3f61961ea9ac7707537a01e4bf75a73/lib/Bio/DB/IndexedBase.pm#L804 I don't remember the exact logic intended but should the return be inside the eval to avoid the ambiguity? Here's my...
``` ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Each line of the file must be less than 65,536 characters. STACK: Error::throw STACK: Bio::Root::Root::throw /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::DB::IndexedBase::_check_linelength /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm:757 STACK: Bio::DB::Fasta::_calculate_offsets /home/lgs6452/.conda/envs/exonerate_env/lib/site_perl/5.26.2/Bio/DB/Fasta.pm:227 STACK: Bio::DB::IndexedBase::_index_files...
Hi, I was wondering if there was any way to parse the NCBI Sequin tbl format? It is defined here: https://www.ncbi.nlm.nih.gov/projects/Sequin/table.html I don't _think_ I see any parser for it...
In my own CI unit testing, I install bioperl as a dependency. However, it is difficult to make sure that bioperl installs. I am pretty sure that that BerkeleyDB (Ubuntu:libberkeleydb-perl)...
Hi, I followed the instructions mentioned at http://asia.ensembl.org/info/docs/api/api_installation.html to install Ensembl API. At the end, to test the installation, we are to run the test file ping_ensembl.pl. At this stage,...
I'm getting an error from bioperl that I don't know how to solve. I assume something with my `bioperl` is broken as this code works on a colleagues ComputeCanada account....
When parsing OBO ontology files the following block is causing issues https://github.com/bioperl/bioperl-live/blob/757470f70f0cc64a53576762d47ca88cbfb2f703/lib/Bio/OntologyIO/obo.pm#L248 The error message states that a term has no ID or name, and that the term will be...
I was trying to install Bio::Tree::Tree via cpanm under perl-5.30.3, but the installation fails. The error message is: -> FAIL Installing XML::DOM::XPath failed. See /home/stud/ga42vor/.cpanm/work/1591284525.30081/build.log for details. Retry with --force...
My installation of BIoPerl 1.7.7 failed due to a problem with a test for Bio::Root::HTTPget, which I think is wrong. I get these failures: ``` # Failed test at t/Root/HTTPget.t...
I got the following message after installing **cpan Bio::Tree::Tree** Then I cannot run any script. I will appreciate any comments to fix this, please. Test Summary Report ------------------- t/test_non_ascii.t (Wstat:...
