Bio::SeqIO::raw - raw sequence file 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 raw 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.
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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
Ewan Birney E<lt>birney@ebi.ac.ukE<gt> Lincoln Stein E<lt>lstein@cshl.orgE<gt>
Jason Stajich E<lt>jason@bioperl.org<gt>
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 $seq object into the stream Returns : 1 for success and 0 for error Args : Array of Bio::PrimarySeqI objects
Title : write_qual Usage : $stream->write_qual($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object
Title : variant Usage : $format = $obj->variant(); Function: Get and set method for the sequence variant. For raw sequence, this indicates whether to treat the input as multiple sequences (the default) or as a single sequence. Current values accepted are: 'single' single sequence 'multiple' multiple sequences (default) Returns : string Args : new value, string
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.