[Biopython-dev] [Biopython - Bug #3312] Failing to parse fasta-m10 format generated by lalign36

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu Nov 10 10:10:06 UTC 2011

Issue #3312 has been updated by Peter Cock.

Assignee set to Biopython Dev Mailing List

Thank you - I can reproduce this on the latest Biopython in our repository.

May we include your sample file in Biopython as a unit test please?
Bug #3312: Failing to parse fasta-m10 format generated by lalign36

Author: gahoo lee
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Target version: 

When I parse an alignment created by lalign which is included in FASTA36, I got errors. We got two sequences in each fasta file now, but if one sequence each, there's no error. Here are the codes and error.

@lalign36 -m 10 at.fasta os.fasta >test.aln@

@from Bio import AlignIO
handle = open('test.aln')
for a in AlignIO.parse(handle, "fasta-m10"):
    assert len(a) == 2, "Should be pairwise!"
    print "Alignment length %i" % a.get_alignment_length()
    for record in a:
        print record.seq, record.name, record.id

@Traceback (most recent call last):
  File "R:\Untitled 4.py", line 5, in <module>
    for a in AlignIO.parse(handle, "fasta-m10"):
  File "D:\Program Files\Python\lib\site-packages\Bio\AlignIO\__init__.py", line 371, in parse
    for a in i:
  File "D:\Program Files\Python\lib\site-packages\Bio\AlignIO\FastaIO.py", line 242, in FastaM10Iterator
    yield build_hsp()
  File "D:\Program Files\Python\lib\site-packages\Bio\AlignIO\FastaIO.py", line 106, in build_hsp
    assert query_tags, query_tags
AssertionError: {}@

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