| Bio::SeqIO::gcg(3pm) | User Contributed Perl Documentation | Bio::SeqIO::gcg(3pm) |
Bio::SeqIO::gcg - GCG sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
This object can transform Bio::Seq objects to and from GCG flat file databases.
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.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email: <birney@ebi.ac.uk>
<lstein@cshl.org>
Jason Stajich, jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args :
Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the formatted $seq object into the stream Returns : 1 for success and 0 for error Args : array of Bio::PrimarySeqI object
Title : GCG_checksum
Usage : $cksum = $gcgio->GCG_checksum($seq);
Function : returns a gcg checksum for the sequence specified
This method can also be called as a class method.
Example :
Returns : a GCG checksum string
Argument : a Bio::PrimarySeqI implementing object
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 occurred.
:
Returns : 1 for success, 0 for failure
Args : string containing parsed seq, value of parsed checksum
| 2021-08-15 | perl v5.32.1 |