[Biopython-dev] [Bug 2284] New: Bio.GFF.easy uses Bio.SeqIO.FASTA which is now deprecated

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Apr 29 19:26:18 UTC 2007


           Summary: Bio.GFF.easy uses Bio.SeqIO.FASTA which is now
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

Specifically Bio.SeqIO.FASTA.FastaReader() and Bio.SeqIO.FASTA.FastaWriter()
are used by the following:

function fasta_single()
function fasta_multi()
function fasta_write()
class TempFastaWriter
class TempFastaWriterSingle

I'm not sure about the classes do, the doc-string unit test (and therefore
test_GFF.py) don't cover them.  Maybe we can deprecate/remove them?

Modifiying the functions to use Bio.SeqIO should be trivial.  I'm tempted to
suggest we deprecate/remove the fasta utility functions instead - and
genbank_single() too.

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