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

💖 Bio::T...ipcress(3pm) 💖

okay bestie, gather round, because this is the User Contributed Perl Documentation page for Bio::Tools::ipcress, and it's lowkey iconic ✨

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🦋 NAME

Bio::Tools::ipcress — parse ipcress output and make features 💅

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🌸 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);

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🎀 DESCRIPTION

so this object is literally a parser for ipcress data, and it makes a Bio::SeqFeatureI for every single ipcress hit. you can then process those features, or add them as annotation to an existing Bio::SeqI object when you're doing automated annotation. main character energy fr fr 👑

this module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org). credit where credit is due, periodt 💖

Ipcress is available through Guy Slater's Exonerate package at http://www.ebi.ac.uk/~guy/exonerate/ ✨

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🌈 FEEDBACK

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. no cap. send your comments and suggestions preferably to the Bioperl mailing list — your participation is much appreciated, bestie 🫶

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. the way that so many experienced and reponsive experts will be able look at the problem and quickly address it?? obsessed 😭 and 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 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 - 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 $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 — (none, bestie, it's giving mysterious 🙈)
• Returns — A Bio::SeqFeatureI implementing object, or undef if there are no more features.
• Args — none

💅 source

• Title — source
• Usage — $obj->source($newval)
• Function — (blank, she's keeping it cute and quiet)
• Example — (blank)
• Returns — value of source (a scalar)
• Args — on set, new value (a scalar or undef, optional)

🌸 primary

• Title — primary
• Usage — $obj->primary($newval)
• Function — (blank)
• Example — (blank)
• Returns — value of primary (a scalar)
• Args — on set, new value (a scalar or undef, optional)

🎀 groupclass

• Title — groupclass
• Usage — $obj->groupclass($newval)
• Function — (blank)
• Example — (blank)
• Returns — value of groupclass (a scalar)
• Args — on set, new value (a scalar or undef, optional)

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and that's the whole page, bestie!! 💖 this was perl v5.32.1, dated 2021-08-15, from Bio::T...ipcress(3pm) — slay, go annotate something gorgeous ✨🦋