[Biopython-dev] [Bug 3119] New: Bio.Nexus can't parse file from Prank 100701 (1st July 2010)

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http://bugzilla.open-bio.org/show_bug.cgi?id=3119

           Summary: Bio.Nexus can't parse file from Prank 100701 (1st July
                    2010)
           Product: Biopython
           Version: 1.54
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


I've been updating test_Prank_tool.py to cope with the latest version of Prank,
1 July 2010 from http://www.ebi.ac.uk/goldman-srv/prank/src/prank/

Some changes are simple, such as removing tests using feature of Prank which
have been removed. One test is failing due to some big changes in the NEXUS
output from Prank, and this may be due to a problem with our parser:

>>> from Bio.Nexus import Nexus
>>> n = Nexus.Nexus("output_prank_v100701.nex")
Traceback (most recent call last):
...
Bio.Nexus.Nexus.NexusError: Taxon AK1H_ECOLI: Illegal character / in line: 
(check dimensions / interleaving)

I will attach the file, it is created by the unit test as output.2.nex but
is usually deleted.

Peter


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