Bio::S...rePair(3pm)

💖 Bio::SeqFeature::FeaturePair — the Bio::S...rePair(3pm) page, but make it cute

okay bestie, gather round, because this one is genuinely iconic. it's the Bio::SeqFeature::FeaturePair module, and it does exactly one thing but does it so well: it holds pair feature information, like, for example, blast hits. two features, one little container, main character energy. 🎀

---

✨ SYNOPSIS ✨

my $feat  = Bio::SeqFeature::FeaturePair->new(
    -feature1 => $f1,
    -feature2 => $f2,
);

# Bio::SeqFeatureI methods can be used

my $start = $feat->start;
my $end   = $feat->end;

# Bio::FeaturePair methods can be used
my $hstart = $feat->hstart;
my $hend   = $feat->hend;

my $feature1 = $feat->feature1;  # returns feature1 object

like. look at it. it's giving effortless. 🦋

---

🌸 DESCRIPTION 🌸

so here's the vibe: this is a sequence feature object where the feature is itself a feature on another sequence. think of a blast hit — residues 1-40 of a protein sequence SW:HBA_HUMAN have hit to bases 100 - 220 on a genomic sequence HS120G22. 💫

the way that works is: the genomic sequence coordinates get used to create one sequence feature $f1, and the protein coordinates get used to create feature $f2. then you just... make a FeaturePair object out of both of them. obsessed.

my $fp = Bio::SeqFeature::FeaturePair->new(
    -feature1 => $f1,   # genomic
    -feature2 => $f2,   # protein
);

this object can be used as a standard Bio::SeqFeatureI, in which case:

my $gstart = $fp->start  # returns start coord on feature1 - genomic seq.
my $gend   = $fp->end    # returns end coord on feature1.

in general, standard Bio::SeqFeatureI method calls return information in feature1. 🫶

data in the feature 2 object are generally obtained using the standard methods prefixed by h (for hit! — yes, that's the whole reason, it's so good):

my $pstart = $fp->hstart # returns start coord on feature2 = protein seq.
my $pend   = $fp->hend   # returns end coord on feature2.

if you wish to swap feature1 and feature2 around:

$feat->invert

so...

$feat->start # etc. returns data in $feature2 object

⚠️ no sub_SeqFeatures or tags can be stored in this object directly, bestie. any features or tags are expected to be stored in the contained objects feature1 and feature2. periodt. 💅

---

💌 CONTACT 💌

Ewan Birney <birney@sanger.ac.uk>

---

📖 APPENDIX 📖

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

🧚 new

• Title : new
• Usage :
• Function : Constructor for this module. Accepts the following parameters:
  • -feature1 — Bio::SeqFeatureI-compliant object
  • -feature2 — Bio::SeqFeatureI-compliant object
  • -feature_factory — Bio::Factory::ObjectFactoryI compliant object to be used when feature1 and/or feature2 are accessed without explicitly set before. This is mostly useful for derived classes who want to set their preferred class for feature objects.
• Example :
• Returns :
• Args : see above

💜 feature1

• Title : feature1
• Usage :

$f = $featpair->feature1
$featpair->feature1($feature)

• Function : Get/set for the query feature
• Returns : Bio::SeqFeatureI
• Args : Bio::SeqFeatureI

💜 feature2

• Title : feature2
• Usage :

$f = $featpair->feature2
$featpair->feature2($feature)

• Function : Get/set for the hit feature
• Returns : Bio::SeqFeatureI
• Args : Bio::SeqFeatureI

✨ start

• Title : start
• Usage :

$start = $featpair->start
$featpair->start(20)

• Function : Get/set on the start coordinate of feature1
• Returns : integer
• Args : [optional] beginning of feature

✨ end

• Title : end
• Usage :

$end = $featpair->end
$featpair->end($end)

• Function : get/set on the end coordinate of feature1
• Returns : integer
• Args : [optional] ending point of feature

🎀 strand

• Title : strand
• Usage :

$strand = $feat->strand()
$feat->strand($strand)

• Function : get/set on strand information, being 1,-1 or 0
• Returns : -1,1 or 0
• Args : [optional] strand information to set

🎀 location

• Title : location
• Usage :

$location = $featpair->location
$featpair->location($location)

• Function : Get/set location object (using feature1)
• Returns : Bio::LocationI object
• Args : [optional] LocationI to store

🦋 score

• Title : score
• Usage :

$score = $feat->score()
$feat->score($score)

• Function : get/set on score information
• Returns : float
• Args : none if get, the new value if set

🦋 frame

• Title : frame
• Usage :

$frame = $feat->frame()
$feat->frame($frame)

• Function : get/set on frame information
• Returns : 0,1,2
• Args : none if get, the new value if set

🌸 primary_tag

• Title : primary_tag
• Usage :

$ptag = $featpair->primary_tag

• Function : get/set on the primary_tag of feature1
• Returns : 0,1,2
• Args : none if get, the new value if set

🌸 source_tag

• Title : source_tag
• Usage :

$tag = $feat->source_tag()
$feat->source_tag('genscan');

• Function : Returns the source tag for a feature, eg, 'genscan'
• Returns : a string
• Args : none

🌈 seqname

• Title : seqname
• Usage :

$obj->seq_id($newval)

• Function : There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the seqname.

This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found.

• Returns : value of seqname
• Args : newvalue (optional)

🌈 hseqname

• Title : hseqname
• Usage :

$featpair->hseqname($newval)

• Function : Get/set method for the name of feature2.
• Returns : value of $feature2->seq_id
• Args : newvalue (optional)

💅 hstart

• Title : hstart
• Usage :

$start = $featpair->hstart
$featpair->hstart(20)

• Function : Get/set on the start coordinate of feature2
• Returns : integer
• Args : none

💅 hend

• Title : hend
• Usage :

$end = $featpair->hend
$featpair->hend($end)

• Function : get/set on the end coordinate of feature2
• Returns : integer
• Args : none

🫶 hstrand

• Title : hstrand
• Usage :

$strand = $feat->strand()
$feat->strand($strand)

• Function : get/set on strand information, being 1,-1 or 0
• Returns : -1,1 or 0
• Args : none

🫶 hscore

• Title : hscore
• Usage :

$score = $feat->score()
$feat->score($score)

• Function : get/set on score information
• Returns : float
• Args : none if get, the new value if set

👑 hframe

• Title : hframe
• Usage :

$frame = $feat->frame()
$feat->frame($frame)

• Function : get/set on frame information
• Returns : 0,1,2
• Args : none if get, the new value if set

👑 hprimary_tag

• Title : hprimary_tag
• Usage :

$ptag = $featpair->hprimary_tag

• Function : Get/set on the primary_tag of feature2
• Returns : 0,1,2
• Args : none if get, the new value if set

⭐ hsource_tag

• Title : hsource_tag
• Usage :

$tag = $feat->hsource_tag()
$feat->source_tag('genscan');

• Function : Returns the source tag for a feature, eg, 'genscan'
• Returns : a string
• Args : none

🔥 invert

• Title : invert
• Usage :

$tag = $feat->invert

• Function : Swaps feature1 and feature2 around
• Returns : Nothing
• Args : none

💖 feature_factory

• Title : feature_factory
• Usage :

$obj->feature_factory($newval)

• Function : Get/set the feature object factory for this feature pair.

The feature object factory will be used to create a feature object if feature1() or feature2() is called in get mode without having been set before.

The default is an instance of Bio::Factory::ObjectFactory and hence allows the type to be changed dynamically at any time.

• Example :
• Returns : The feature object factory in use (a Bio::Factory::ObjectFactoryI compliant object)
• Args : on set, a Bio::Factory::ObjectFactoryI compliant object

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and that's the whole page, bestie, no notes. 💀✨

this lil doc lives in the User Contributed Perl Documentation collection, and it's running on perl v5.32.1, dated 2021-08-15 — that's the Bio::S...rePair(3pm) footer energy right there. go forth and pair your features. 🦋💖🎀