Bio::Tools::EPCR(3pm)

✨ Bio::Tools::EPCR ✨

okay bestie, so this is Bio::Tools::EPCR from the User Contributed Perl Documentation collection — a whole module that parses ePCR output and turns it into features 💖

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🌸 NAME 🌸

Bio::Tools::EPCR — literally parses ePCR output and makes features out of it. that's the whole vibe. 🧚

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🦋 SYNOPSIS 🦋

a simple annotation pipeline wrapper for ePCR data — assuming your ePCR data is already generated in the file seq1.epcr, and your sequence data is in fasta format in a file called seq1.fa:

# 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);

see like, that's it. you parse, you grab features, you slap them onto your sequence, you write it out. iconic behavior tbh 💅

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💜 DESCRIPTION 💜

so this object is a parser for ePCR data, and for every single ePCR hit it creates a Bio::SeqFeatureI. 🎀

then you can either process those features, or add them as annotation to an existing Bio::SeqI object — which is the whole point, because that's how you do automated annotation. ✨

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is, like, an integral part of the evolution of this module and all the other Bioperl modules. no cap. so please 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 🌈

okay so real talk — please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

rather than hitting up the module maintainer directly, bestie 😭 the thing is there are many experienced and responsive experts on that list who will be able to look at your problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible — the more detail the better fr fr.

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Jason Stajich 👑

email: jason-at-bioperl.org

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🍓 APPENDIX 🍓

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk 🔥).

✨ new ✨

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'.

let me break the args down for you bestie, because there's a lil either/or situation going on here 👀

• -fh — a filehandle. OR ⬇️
• -file — a filename. (pick one, not both, we're not chaotic like that)
• -primary — a string that becomes the common value for each feature's -primary tag. defaults to 'sts'. and this in turn maps to the GFF 'type' tag (aka 'method'). 💫
• -source — a string that becomes the common value for each feature's -source tag. defaults to 'e-PCR'. this one in turn maps to the GFF 'source' tag. 🌸
• -groupclass — a string that's 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

it hands you the next feature in the analysis result, or undef when there are literally no more features left. no args, it just does its thing. 🦋

⭐ 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)

returns the value of source (a scalar), and on set you pass the 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)

same energy, different attribute — returns the value of primary (a scalar), and on set, the 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)

returns the value of groupclass (a scalar), on set you hand it the new value (a scalar or undef, optional). that's the trio, all three accessors, same pattern, slay. 💜

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ngl the Function: and Example: fields up there are just... empty in the original. not me leaving them exactly as they were bestie, I'm just being faithful 🫶

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and that's the whole page!! periodt 💅✨ this was perl v5.32.1, dated 2021-08-15, from Bio::Tools::EPCR(3pm) — love that for us, mwah, go annotate something gorgeous 🎀🦋💖