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

🧬 Bio::D...::Kseq(3pm) — bestie edition

okay so this is a page from the User Contributed Perl Documentation and it's literally the manual for Bio::D...::Kseq(3pm) 💅 it's a Perl module page, the vibe is very "I read FASTA/FASTQ files for breakfast", and we're gonna go through every single bit together. grab a boba. 🧋

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📜 LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

fr fr, that's the whole license text, don't skip it, the lawyers are watching 👀

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✨ NAME ✨

Bio::DB::HTS::Kseq — Bindings to Kseq 🦋

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🌸 DESCRIPTION 🌸

So what is this? It's bindings to the Kseq library, and its whole personality is iterating through a locally held FASTA/FASTQ file very quickly. like, speed. 💨

It supports compressed and uncompressed files, and it also handles filehandles alongside them. so many options bestie, we love versatility 🫶

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🎀 SYNOPSIS 🎀

here's the whole vibe in code, exactly as written:

my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');
my $iter = $kseq->iterator();
while(my $r = $iter->next_seq()) {
  say $r->name;
  say $r->desc;
  say $r->seq;
  say $r->qual;
}

# Allowing the object to go out of scope will close down all file handles

heads up: letting the object go out of scope closes down all the file handles. it's giving "clean up after yourself" energy 🧹✨

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💅 METHODS 💅

⭐ new

my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');

Returns an instance of this object from a file path. that's it, that's the whole job. iconic.

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⭐ newfh

open my $fh, '<', 'path' or die "Cannot open path: $!";
binmode $fh;
my $kseq = Bio::DB::HTS::Kseq->newfh($fh);

Returns an instance of this object from an opened file handle. and the way that it supports any known Perl glob/filehandle type?? obsessed. 😭💖

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⭐ iterator

my $iter = $kseq->iterator();

Returns the kseq iterator object. this is your main character — it's the thing you loop over. periodt. 👑

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that's the whole page bestie, every option, every snippet, no cap, nothing skipped 💯

sign-off time 🌈 — this beauty was rendered by perl v5.40.0, dated 2024-10-31, and it lives at the title Bio::D...::Kseq(3pm). go read some sequences, you ate. 🍓🧚💜