Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables
Used by Bio::SeqIO::EMBL to help process the Feature Table
Represents one particular Feature with the following fields
key - the key of the feature loc - the location string of the feature <other fields> - other fields
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 bioperl-guts-l@bioperl.org - Automated bug and CVS messages http://bioperl.org/MailList.shtml - 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 birney@sanger.ac.uk
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : from_SeqFeature Usage : @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$context_annseq); Function: constructor of fthelpers from SeqFeatures : : The additional annseq argument is to allow the building of FTHelper : lines relevant to particular sequences (ie, when features are spread over : enteries, knowing how to build this) Returns : an array of FThelpers Args : seq features
Title : _generic_seqfeature Usage : $fthelper->_generic_seqfeature($annseq, "GenBank") Function: processes fthelper into a generic seqfeature Returns : TRUE on success and otherwise FALSE Args : Bio::Seq, string indicating the source (GenBank/EMBL/SwissProt)
Title : _parse_loc Usage : $fthelper->_parse_loc($feature, $loc_string) Function: Parses the given location string and sets start() and end() in the given feature object appropriately. As side effects, tag values (private) for features where only partial locations are given may be set. These tags are prefixed with an underscore, and are not included in the FTHelper object generated by the from_SeqFeature method. Note that this method is private. Returns : TRUE on success and otherwise FALSE Args : Bio::SeqFeatureI, string
Title : key Usage : $obj->key($newval) Function: Example : Returns : value of key Args : newvalue (optional)
Title : loc Usage : $obj->loc($newval) Function: Example : Returns : value of loc Args : newvalue (optional)
Title : field Usage : Function: Example : Returns : Args :
Title : add_field Usage : Function: Example : Returns : Args :
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.