NAME¶
Bio::SeqIO::FTHelper - Helper class for EMBL/Genbank feature tables
SYNOPSIS¶
Used by Bio::SeqIO::EMBL,Bio::SeqIO::genbank, and Bio::SeqIO::swiss to help
process the Feature Table
DESCRIPTION¶
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
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
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.
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 the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Ewan Birney¶
Email birney@ebi.ac.uk
CONTRIBUTORS¶
Jason Stajich jason@bioperl.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
_generic_seqfeature¶
Title : _generic_seqfeature
Usage : $fthelper->_generic_seqfeature($annseq, "GenBank")
Function: processes fthelper into a generic seqfeature
Returns : TRUE on success and otherwise FALSE
Args : The Bio::Factory::LocationFactoryI object to use for parsing
location strings. The ID (e.g., display_id) of the sequence on which
this feature is located, optionally a string indicating the source
(GenBank/EMBL/SwissProt)
from_SeqFeature¶
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
key¶
Title : key
Usage : $obj->key($newval)
Function:
Example :
Returns : value of key
Args : newvalue (optional)
loc¶
Title : loc
Usage : $obj->loc($newval)
Function:
Example :
Returns : value of loc
Args : newvalue (optional)
field¶
Title : field
Usage :
Function:
Example :
Returns :
Args :
add_field¶
Title : add_field
Usage :
Function:
Example :
Returns :
Args :