Bio::Variation::IO::flat - flat file sequence variation input/output stream
Do not use this module directly. Use it via the Bio::Variation::IO class.
This object can transform Bio::Variation::SeqDiff objects to and from flat file databases. The format used is EMBL like extension of what is used by the "EBI Mutation Checker" at http://www.ebi.ac.uk/cgi-bin/mutations/check.cgi and will eventually replace it.
More information of the attributes and values use can be found at http://www.ebi.ac.uk/mutations/recommendations/.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists
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/
Email: heikki@ebi.ac.uk Address:
EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next Usage : $haplo = $stream->next() Function: returns the next seqDiff in the stream Returns : Bio::Variation::SeqDiff object Args : NONE
Title : write Usage : $stream->write(@seqDiffs) Function: writes the $seqDiff object into the stream Returns : 1 for success and 0 for error Args : Bio::Variation::SeqDiff object
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.