[Bioperl-guts-l] [Bug 2197] New: Bio::Species throws if species name is synonym of lineage

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jan 29 08:24:41 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2197

           Summary: Bio::Species throws if species name is synonym of
                    lineage
           Product: Bioperl
           Version: main-trunk
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: roy at colibase.bham.ac.uk


I'm having problems similar to those discussed in this thread:
http://comments.gmane.org/gmane.comp.lang.perl.bio.general/13766

and in bug 2092.

I'm using the 1.52 release code, that includes Sendu's fix for the 
problem, but I'm still getting errors with some species names. The 
process seems to fall foul of line 167 of Bio::Species, which checks 
that the lineage starts at the species in question.

Here are some of the error messages I'm getting:

Uniprot entry P21215:
MSG: The supplied lineage does not start near 'Clostridium sp.' (I was 
supplied 'sp. ATCC29733 | Clostridium | Clostridiaceae | Clostridiales | 
Clostridia | Firmicutes | Bacteria')

Uniprot entry Q98AM7:
MSG: The supplied lineage does not start near 'Rhizobium loti' (I was 
supplied 'loti | Mesorhizobium | Phyllobacteriaceae | Rhizobiales | 
Alphaproteobacteria | Proteobacteria | Bacteria')

Genbank entry CP000026:
MSG: The supplied lineage does not start near 'Salmonella enterica 
subsp. enterica serovar Paratyphi A str. ATCC 9150' (I was supplied 
'paratyphi | Salmonella | Enterobacteriaceae | Enterobacteriales | 
Gammaproteobacteria | Proteobacteria | Bacteria')

It is easy to see why problems are arising- the species name used in the 
GenBank/Uniprot entry is sometimes a synonym of that in the supplied 
lineage, rather than an exact duplicate. Is the check on line 167 really 
necessary? Or at least could the throw be changed to a warn?


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