[Biopython-dev] [Bug 2745] New: Bio.GenBank.LocationParserError with a GenBank CON file

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2745

           Summary: Bio.GenBank.LocationParserError with a GenBank CON file
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


The following file has a Bio.GenBank.LocationParserError:
ftp://ftp.ncbi.nih.gov/genbank/daily-nc/con_nc.0103.flat.gz

Partial error message (as the last line is the complete CONTIG line).

Syntax error at or near `Tokens('close_paren')' token                           
Traceback (most recent call last):                                              
  File "parse_gbk.py", line 26, in <module>                                     
    for record in SeqIO.parse(handle, "genbank") :                              
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/Scanner.py",
line 410, in parse_records                                
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/Scanner.py",
line 393, in parse                                        
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/Scanner.py",
line 371, in feed                                         
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/Scanner.py",
line 1093, in _feed_misc_lines                            
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/__init__.py",
line 990, in contig_location                             
  File
"/home/bsouthey/python/biopython_cvs/biopython/build/lib.linux-x86_64-2.5/Bio/GenBank/__init__.py",
line 707, in location                                    
Bio.GenBank.LocationParserError:
join(DS483543.1:1..325170,gap(unk100),DS483544.1:1..218545,gap(unk100),DS483545.1:1..95394,gap(unk100),DS483546.1:1..261305,gap(unk100),DS483547.1:1..63422,gap(unk100),DS483548.1:1..77432,gap(unk100),DS483549.1:1..371434,gap(unk100),DS483550.1:1..74569,gap(unk100),DS483551.1:1..54637,gap(unk100),DS483552.1:1..73591,gap(unk100),DS483553.1:1..63632,gap(unk100),DS483554.1:1..60619,gap(unk100),DS483555.1:1..57196,gap(unk100),DS483556.1:1..95189,gap(unk100),DS483557.1:1..48586,gap(unk100),DS483558.1:1..45971,gap(unk100),DS483559.1:1..59826,gap(unk100),DS483560.1:1..49535,gap(unk100),DS483561.1:1..51083,gap(unk100),...


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