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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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updates for biopython 1.82 #141

Closed fubar2 closed 8 months ago

fubar2 commented 9 months ago

@chapmanb Hi Brad, Firstly, thanks for maintaining bcbb! Helena used GFF to write gff files parse from blastxml in the Galaxy JBrowse1 tool. In updating for JBrowse2, it turns out that the biopython 1.82 updates break the GFF test, writer and parser.

Easier to fix this otherwise working code than adopt any of the newer GFF repositories - so this PR:

  1. fixes _nofuzzystart and end deprecation
  2. moves all strand= in seqfeatures into simplelocations
  3. Passes tests and fixes https://github.com/galaxyproject/tools-iuc/pull/5695#issuecomment-1874637212
chapmanb commented 8 months ago

Thank you so much for this fix and apologies about missing this earlier. Merging all of these bitrot fixes and I'll release a new version.

fubar2 commented 8 months ago

Many thanks, @chapmanb - heavily used in Helena's JBrowse code for making specialised GFF for blastxml and MAF - this will get plenty of use...