table of contents
| Bio::Tools::ipcress(3pm) | User Contributed Perl Documentation | Bio::Tools::ipcress(3pm) |
NAME¶
Bio::Tools::ipcress - Parse ipcress output and make features
SYNOPSIS¶
# A simple annotation pipeline wrapper for ipcress data
# assuming ipcress data is already generated in file seq1.ipcress
# and sequence data is in fasta format in file called seq1.fa
use Bio::Tools::ipcress;
use Bio::SeqIO;
my $parser = Bio::Tools::ipcress->new(-file => 'seq1.ipcress');
my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa');
my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");
while( my $feat = $parser->next_feature ) {
# add ipcress annotation to a sequence
$seq->add_SeqFeature($feat);
}
my $seqout = Bio::SeqIO->new(-format => 'embl');
$seqout->write_seq($seq);
DESCRIPTION¶
This object serves as a parser for ipcress data, creating a Bio::SeqFeatureI for each ipcress hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation.
This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org).
Ipcress is available through Guy Slater's Exonerate package http://www.ebi.ac.uk/~guy/exonerate/
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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Sheldon McKay¶
Email mckays@cshl.edu
APPENDIX¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new¶
Title : new
Usage : my $ipcress = Bio::Tools::ipcress->new(-file => $file,
-primary => $fprimary,
-source => $fsource,
-groupclass => $fgroupclass);
Function: Initializes a new ipcress parser
Returns : Bio::Tools::ipcress
Args : -fh => filehandle
OR
-file => filename
-primary => a string to be used as the common value for
each features '-primary' tag. Defaults to
the sequence ontology term 'PCR_product'.
(This in turn maps to the GFF 'type'
tag (aka 'method')).
-source => a string to be used as the common value for
each features '-source' tag. Defaults to
'ipcress'. (This in turn maps to the GFF 'source'
tag)
-groupclass => a string to be used as the name of the tag
which will hold the sts marker namefirst
attribute. Defaults to 'name'.
next_feature¶
Title : next_feature
Usage : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
source¶
Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source (a scalar) Args : on set, new value (a scalar or undef, optional)
primary¶
Title : primary Usage : $obj->primary($newval) Function: Example : Returns : value of primary (a scalar) Args : on set, new value (a scalar or undef, optional)
groupclass¶
Title : groupclass Usage : $obj->groupclass($newval) Function: Example : Returns : value of groupclass (a scalar) Args : on set, new value (a scalar or undef, optional)
| 2021-08-15 | perl v5.32.1 |