search

bioperl / bioperl-live-redmine

Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
0 stars 0 forks source link

Problems with Bio::LocatableSeq::length() and strand() #87

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Chris Fields (@cjfields) Original Redmine Issue: 3129, https://redmine.open-bio.org/issues/3129 Original Date: 2010-08-03 Original Assignee: Chris Fields

While fixing bug 2984, I noticed Bio::LocatableSeq is wrong when calculating length (it is returning the string length, not end - start + 1) and strand() is inconsistent (not one of 0, –1, +1). Fixing the problem within LocatableSeq leads to test failures elsewhere.

Have added a couple of tests for this in t/AlignIO/phylip.t. This may have to wait for the GSoC project to finish up.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2011-07-17T14:26:54Z

Pushing this to the front, will attempt fixing on main trunk. Bio::LocatableSeq should also be moved into Bio::Range or into it’s own repo (maybe along with other related modules).