[Debian-med-packaging] Bug#848735: pynast: FTBFS: Test failures

[Aaron M. Ucko]

Andreas Tille <tille at debian.org> writes:

>    ncbi-blast+-legacy (>= 2.5.0-2~) | blast2

Yes, this is an appropriate dependency for anything that historically
listed blast2 and continues to use legacy command names such as bl2seq.

> Could you give some hint for a patch to fix this test suite error:

Good question.  The error from the underlying blastn command (buried in
the middle of the log) is

  BLAST engine error: Error: Gap existence and extension values 0 and 0 are not supported for substitution scores 1 and -1
  3 and 2 are supported existence and extension values
  2 and 2 are supported existence and extension values
  1 and 2 are supported existence and extension values
  0 and 2 are supported existence and extension values
  4 and 1 are supported existence and extension values
  3 and 1 are supported existence and extension values
  2 and 1 are supported existence and extension values
  4 and 2 are supported existence and extension values
  Any values more stringent than 4 and 2 are supported

I've tried fiddling with parameters to address this error, but so far
haven't been able to get blastn to report *any* hits for these test
cases, perhaps because the sequences are too short.

I'm also concerned that pynast.util.blast_align_unaligned_seqs invokes
bl2seq with the -VT flag, which historically requested the old BLAST
engine.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu