[Biopython-dev] [Bug 1531] New: Bio.Fasta.RecordParser, SequenceParser

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

http://bugzilla.bioperl.org/show_bug.cgi?id=1531

           Summary: Bio.Fasta.RecordParser, SequenceParser
           Product: Biopython
           Version: Not Applicable
          Platform: Sun
        OS/Version: SunOS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: ktdiedrich at yahoo.com


The Bio.Fasta RecordParser and SequenceParser can only handle
FASTA sequence files with spaces between the records ie
> name 1
aggcgcgatcgatg
cgagcatcagcgag
acgata

> name 2
aaggcttagcatcg
cacgcatcaa

But many FASTA sequence files are statcked together
> name 1
aggcgcgatcgatg
cgagcatcagcgag
acgata
> name 2
aaggcttagcatcg
cacgcatcaa


They also can't hangle empty lines at the beginning of the FastaSequence file. 

The error occurs in line 300 Bio/ParserSupport.py

The RecordParser.parse() definition also doesn't advance the file handle
position when it gets to the end of the file handle. It keeps returning the last
record so a loop reading records never ends.



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