Bio::D...ignment(3pm)

💖 Bio::D...ignment(3pm) 💖

okay bestie, so this is the manual page for Bio::DB::GFF::Aggregator::alignment, living its best life in the User Contributed Perl Documentation, and it's filed under the page name Bio::D...ignment(3pm) because apparently someone was in a hurry when they named the file. anyway. it slays.

---

✨ NAME ✨

Bio::DB::GFF::Aggregator::alignment — the Alignment aggregator. that's it, that's the name, she's simple and she knows it 💅

---

🌸 SYNOPSIS 🌸

here's how you'd actually use her:

use Bio::DB::GFF;

# Open the sequence database
my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                 -dsn     => 'dbi:mysql:elegans42',
                                 -aggregator => ['alignment'],
                               );

-----------------------------
Aggregator method: alignment
Main method:       (none)
Sub methods:       nucleotide_match,EST_match,cDNA_match,expressed_sequence_match,
                   translated_nucleotide_match,protein_match,HSP
-----------------------------

look at those sub methods. a whole roster. she's got range 🌈

---

🦋 DESCRIPTION 🦋

Bio::DB::GFF::Aggregator::alignment is one of the default aggregators, and ngl she was written to be compatible with the C elegans GFF files. her whole thing is taking raw "similarity" features and aggregating them into composite features of type "alignment". and honestly? a better name for this class might be "gapped_alignment." the original author said it, not me 🙈

here's the tea though: this aggregator does not insist that there be a single top-level feature spanning one end of the alignment all the way to the other. and the way that plays out is — it can produce truncated alignments if the entire alignment isn't contained within the segment of interest. so like, keep that in mind. it's giving "close enough" energy 😭

---

👑 aggregate

• Title — aggregate
• Usage — $features = $a->aggregate($features,$factory)
• Function — aggregate a feature list into composite features
• Returns — an array reference containing modified features
• Args — see L<Bio::DB::GFF::Aggregator>
• Status — Public

so because there are so many similarity features (like, an unhinged amount), the aggregate() method gets overridden in here purely to do some optimizations. speed demon behavior fr fr 🔥

---

🎀 method

• Title — method
• Usage — $aggregator->method
• Function — return the method for the composite object
• Returns — the string "alignment"
• Args — none
• Status — Public

she returns "alignment". consistent queen 💖

---

🧚 part_names

• Title — part_names
• Usage — $aggregator->part_names
• Function — return the methods for the sub-parts
• Returns — the full list of aggregated methods
• Args — none
• Status — Public

all the sub methods, all together, one big happy family 🫶

---

lowkey reminder bestie: the truncated-alignment thing is real. if your alignment isn't fully inside the segment you're looking at, you're getting a partial one. no cap.

---

and that's the whole page 💜 this one shipped with perl v5.30.0 and is dated 2020-01-13, so go forth, aggregate your similarities, and stay iconic ✨👑💅