| Bio::Tools::EPCR(3pm) | User Contributed Perl Documentation | Bio::Tools::EPCR(3pm) |
Bio::Tools::EPCR - Parse ePCR output and make features
# A simple annotation pipeline wrapper for ePCR data
# assuming ePCR data is already generated in file seq1.epcr
# and sequence data is in fasta format in file called seq1.fa
use Bio::Tools::EPCR;
use Bio::SeqIO;
my $parser = Bio::Tools::EPCR->new(-file => 'seq1.epcr');
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 EPCR 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 ePCR data, creating a Bio::SeqFeatureI for each ePCR hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $epcr = Bio::Tools::EPCR->new(-file => $file,
-primary => $fprimary,
-source => $fsource,
-groupclass => $fgroupclass);
Function: Initializes a new EPCR parser
Returns : Bio::Tools::EPCR
Args : -fh => filehandle
OR
-file => filename
-primary => a string to be used as the common value for
each features '-primary' tag. Defaults to
'sts'. (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
'e-PCR'. (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)
| 2021-08-15 | perl v5.32.1 |