[Biojava-dev] [Bug 3140] New: Required Correction in GenbankLocationParser class

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3140

           Summary: Required Correction in GenbankLocationParser class
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


Reported on behalf of Deepak Sheoran:

Their is problem with GenbankLocationParser class, this class don't process
genbank record with    Accession: M32882. LocationParser class fails at
following line in genbank record:

    gene  </nuccore/150738?itemid=33&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
    mRNA  </nuccore/150738?itemid=15&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
                    /note="alternative transcript"


Exception stack trace is as follows:

       Could not understand position: 10206,1..855
       org.biojava.bio.seq.io.ParseException: Could not understand position:
10206,1..855
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:277)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:244)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131)

I did some investigation in following matter, and found the defect in regular
expression named as "gp" in GenbankLocationParser class.

This error can be fixed by applying attached patch. And then for testing I have
created a method which proves that it can now understand all the possible
combination of location. This test class is also attached so that you can test
my patch before and after its application.


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