Bio::T...R::Set(3pm)

💖 NAME 💖

Bio::Tools::HMMER::Set — literally a whole set of identical domains from your HMMER matches, bestie 🦋

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✨ SYNOPSIS ✨

# get a Set object probably from the results object
print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

foreach $domain ( $set->each_Domain ) {
    print "Domain start ",$domain->start," end ",$domain->end,"\n";
}

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🌸 DESCRIPTION 🌸

Okay so picture this: a set of HMMER domains that all hit one single sequence. HMMER is out here reporting two different kinds of scores — there's a per sequence total score (plus its evalue) and a per domain score and evalue. And this object? It's giving a collection of the same domain, but carrying the sequence bits score and evalue along with it. (these attributes are also on the per domain scores, which you can get there). Periodt. 💅

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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 one of the Bioperl mailing lists. Your participation is much appreciated, fr fr.

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.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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 - Ewan Birney 👑

Email birney-at-ebi.ac.uk

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 💀

add_Domain

• Title : add_Domain
• Usage : $set->add_Domain($domain)
• Function: adds the domain to the list
• Returns : nothing
• Args : A Bio::Tools::HMMER::Domain object

each_Domain

• Title : each_Domain
• Usage : foreach $domain ( $set->each_Domain() )
• Function: returns an array of domain objects in this set
• Returns : array
• Args : none

name

• Title : name
• Usage : $obj->name($newval)
• Function:
• Example :
• Returns : value of name
• Args : newvalue (optional)

desc

• Title : desc
• Usage : $obj->desc($newval)
• Function:
• Example :
• Returns : value of desc
• Args : newvalue (optional)

accession

• Title : accession
• Usage : $obj->accession($newval)
• Function:
• Example :
• Returns : value of accession
• Args : newvalue (optional)

bits

• Title : bits
• Usage : $obj->bits($newval)
• Function:
• Example :
• Returns : value of bits
• Args : newvalue (optional)

evalue

• Title : evalue
• Usage : $obj->evalue($newval)
• Function:
• Example :
• Returns : value of evalue
• Args : newvalue (optional)

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and that's the whole page bestie, mwah 💋 this lil' thing shipped with perl v5.30.0, dated 2019-10-29, and it lives under the name Bio::T...R::Set(3pm) — go forth and slay your domain sets 🧚✨💜