Bio::T...::isPcr(3pm)

💖 Bio::Tools::isPcr — bestie edition 💖

okay so this is the manual page for Bio::Tools::isPcr, part of the User Contributed Perl Documentation — and yes the title is literally abbreviated as Bio::T...::isPcr(3pm) because perl is dramatic like that. 💅

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✨ NAME ✨

Bio::Tools::isPcr — parse isPcr output and make features 🧬

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🌸 SYNOPSIS 🌸

    # 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);

heads up bestie: the comment in there is doing a lot of heavy lifting. this parser is for the default fasta output from isPcr. bed and psl output formats are not supported. no cap. 🚫

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🦋 DESCRIPTION 🦋

This object is literally a parser for isPcr data (in the default fasta format), and what it does is create a Bio::SeqFeatureI for each isPcr hit. those features can then be processed, or added as annotation to an existing Bio::SeqI object, for automated annotation purposes. iconic behaviour fr. ✨

This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org). giving credit where credit is due, we love to see it 🫶

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📬 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.

bestie pls do NOT slide into the maintainer's DMs directly, the mailing list has the experts and they will fix you up. include code + data examples or it's giving "it doesn't work" with zero context 😭

🐛 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

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👑 AUTHOR — Sheldon McKay 👑

Email mckays@cshl.edu

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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 $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'.

so like, this is where you birth a brand new isPcr parser into the world 🌱 here's the tea on the args:

• -fh — a filehandle
  • OR
• -file — a filename
• -primary — a string that becomes the common value for each feature's -primary tag. Defaults to the sequence ontology term 'PCR_product'. (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 'isPcr'. (This in turn maps to the GFF 'source' tag.)
• -groupclass — a string used as the name of the tag which will hold the sts marker namefirst attribute. Defaults to 'name'.

yes namefirst is written exactly like that in the original, I am simply the messenger 🫡

💫 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

the vibe: call it, get the next feature, or get undef when there are no more features left. no args, no drama. 💅

💫 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)

getter/setter situation ✨ — returns the value of source, which is a scalar, and if you pass a new value (a scalar, or undef, optional) it sets it.

💫 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 as source but for primary 💜 returns the value of primary (a scalar); 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)

and the trio is complete 🎀 returns the value of groupclass (a scalar); on set, the new value (a scalar or undef, optional).

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okay that's the whole page bestie, you ate it 💅✨ this doc was served to you by perl v5.32.1, dated 2021-08-15, straight from the Bio::T...::isPcr(3pm) manual. go forth and annotate, icon 👑🦋