NAME

Bio::SeqIO::GCG - Raw sequence input/output stream

SYNOPSIS

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
    }

DESCRIPTION

This object can transform Bio::Seq objects to and from GCG-formatted sequence files.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHORS - Ewan Birney & Chris Dagdigian

Email birney@sanger.ac.uk, dag@sonsorol.org

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.

APPENDIX

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