search

ofanoyi / pygr

Automatically exported from code.google.com/p/pygr
0 stars 0 forks source link

undefined 'al' in NLMSA.add_aligned_intervals #74

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
hi, here's a test script which i believe shows a bug in latest pygr from
git://repo.or.cz/pygr:

{{{

from pygr import seqdb, cnestedlist
msa = cnestedlist.NLMSA('s', mode='memory',
                pairwiseMode=True, bidirectional=True)
msa.add_aligned_intervals(alignedIvals=[], alignedIvalsAttrs={})

}}}

even when given real args for alignedIvals and Attrs, the al never exists
so it always fails.
http://repo.or.cz/w/pygr.git?a=blob;f=pygr/nlmsa_utils.py;h=25c07efb13dcbdb08e7c
2ac12c6de5334c544a1a;hb=HEAD#l355

i can get around it by specifying a srcDB and destDB

Original issue reported on code.google.com by bpederse on 23 Mar 2009 at 9:27

GoogleCodeExporter commented 8 years ago 
Fixed in issue #40; see branch 
http://github.com/ctb/pygr/commits/review_issue40.

Thanks!

Original comment by the.good...@gmail.com on 24 Mar 2009 at 10:42