bioperl-live
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bioperl
Core BioPerl 1.x code
See this link (may need to join MAKER list): https://groups.google.com/d/topic/maker-devel/l3HmeRfgKjU/discussion Letter reproduced below. The error seems to be a seq ID evaluating as FALSE. Dear Maker, I did run maker...
Some time ago I made the mistake of uploading to CPAN a module called Bio::Tools::Alignment::Overview, the module wasn't associated to bioperl but for some reason I decided to use the...
When I use Bio::SeqFeature::Tools::Unflattener to convert GenBank flat-feature-list to containment hierarchy, ``` $unflattener->unflatten_seq(-seq=>$seq, -use_magic=>1); ``` Everything is fine except these genes has pseudo tag. 1. Gene and CDS with pseudo...
Old Redmine tickets have been migrated to GitHub in a separate repo for now: https://github.com/bioperl/bioperl-live-redmine/issues These may or may not be merged with this tracker; the original migration was a...
See: http://mailman.open-bio.org/pipermail/bioperl-l/2014-September/088945.html Basically, this works with the August patch for GenBank parsing (so the bug isn't there) but some change since 1.6.922 has caused parsing to slow dramatically. We'll need...
Simplealign
Hi, Chris, This is my implementation of Bio::SimpleAlign. I have a detailed report describing the improvement to the code, and explaining the failed tests using t/Align/SimpleAlign.t. If you need any...
`is_ter_codon` and `is_start_codon` do not behaves the same. ( with that PR now it does). is_ter_codon was not verifying all unambiguous_codons, but only the first. I do not get why...
Fix bugs in codon table: * table 0 was not selectable via `Bio::Tools::CodonTable->new( -id => 0);` but was working only by creating a codon table by default and using the...
The current dist has a minimum version of v5.6 (set at [`t/00-compile.t`](https://metacpan.org/release/CJFIELDS/BioPerl-1.7.8/source/t/00-compile.t#L1)). But as discussed in [this comment](https://github.com/bioperl/bioperl-live/pull/374/files/3a3208f69e76ed79fd47286af94bc85a75e88f1f#r1167635992), the minimum version based on the syntax and features used is v5.8.
Some examples: - , - . This helps with automatically assigning to issues and PRs. Possibly starting with the listing from `git grep "Cared for"`.