Bio::SeqIO::GCG(3pm)

Bio::SeqIO::GCG - Raw sequence input/output stream It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go:

    $stream = Bio::SeqIO->new(-file => $filename, -format => 'GCG');

    while $seq ( <$stream> ) {
        # $seq is a Bio::Seq object
    }

This object can transform Bio::Seq objects to and from GCG-formatted sequence files.
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Email [email protected], [email protected] Ewan Birney wrote the all the base SeqIO stuff. This module is based on his SeqIO::Fasta and has been tweaked by Chris Dagdigian, to support GCG formatted sequence input/output. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

write_seq

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the fromatted $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object, sequence string

_filehandle

 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: 
 Example : 
 Returns : value of _filehandle
 Args    : newvalue (optional)

_validate_checksum

 Title   : _validate_checksum
 Usage   : n/a - internal method
 Function: if parsed gcg sequence contains a checksum field
         : we compare it to a value computed here on the parsed
         : sequence. A checksum mismatch would indicate some
         : type of parsing failure occured.
         :
 Returns : 1 for success, 0 for failure
 Args    : string containing parsed seq, value of parsed cheksum