| Bio::Tools::isPcr(3pm) | User Contributed Perl Documentation | Bio::Tools::isPcr(3pm) |
Bio::Tools::isPcr - Parse isPcr output and make features
# A simple annotation pipeline wrapper for isPcr data
# assuming isPcr data is already generated in file seq1.isPcr
# and sequence data is in fasta format in file called seq1.fa
# Note: this parser is meant for the default fasta output from
# isPcr. bed and psl output formats are not supported.
use Bio::Tools::IsPcr;
use Bio::SeqIO;
my $parser = Bio::Tools::isPcr->new(-file => 'seq1.isPcr');
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 isPcr annotation to a sequence
$seq->add_SeqFeature($feat);
}
my $seqout = Bio::SeqIO->new(-format => 'embl');
$seqout->write_seq($seq);
This object serves as a parser for isPcr data (in the default fasta format), creating a Bio::SeqFeatureI for each isPcr 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).
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
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 of the bugs and their resolution. Bug reports can be submitted via the web:
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Email mckays@cshl.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $ispcr = Bio::Tools::isPcr->new( -file => $file,
-primary => $fprimary,
-source => $fsource,
-groupclass => $fgroupclass);
Function: Initializes a new isPcr parser
Returns : Bio::Tools::isPcr
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
'isPcr'. (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'.
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
Title : source Usage : $obj->source($newval) Function: Example : Returns : value of source (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : primary Usage : $obj->primary($newval) Function: Example : Returns : value of primary (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : groupclass Usage : $obj->groupclass($newval) Function: Example : Returns : value of groupclass (a scalar) Args : on set, new value (a scalar or undef, optional)
| 2020-10-28 | perl v5.30.3 |