Grinde...lection(3pm)

🎀 NAME 🎀

okay so bestie, welcome to Grinder::KmerCollection(3pm) — a User Contributed Perl Documentation situation, and it's giving a collection of kmers from sequences 💖 no cap.

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✨ SYNOPSIS ✨

my $col = Grinder::KmerCollection->new( -k    => 10,
                                        -file => 'seqs.fa' );

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🌸 DESCRIPTION 🌸

So basically this thing manages a collection of kmers that were found in various sequences. It literally stores the info about what sequence a kmer was found in and its starting position on that sequence. It's a whole little filing cabinet for kmers, and honestly? iconic. 💅

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🦋 AUTHOR 🦋

Florent Angly <florent.angly@gmail.com> — thank you for your service, king/queen/monarch 👑

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👑 APPENDIX 👑

The rest of this documentation (aka the main character section) details each of the object methods one by one. Heads up: internal methods are usually preceded with a _ — that underscore is the "do not perceive me" marker 🙈

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🧚 new

• Title: new
• Usage: my $col = Grinder::KmerCollection->new( -k => 10, -file => 'seqs.fa', -revcom => 1 );
• Function: Build a new kmer collection ✨
• Args:
  • -k — set the kmer length (default: 10 bp)
  • -revcom — count kmers before and after reverse-complementing sequences (default: 0)
  • -seqs — count kmers in the provided arrayref of sequences (which are Bio::Seq or Bio::SeqFeature objects)
  • -ids — if specified, index the sequences provided to -seq using the IDs in this arrayref instead of using the sequences' $seq->id() method
  • -file — count kmers in the provided file of sequences
  • -weights — if specified, assign the abundance of each sequence from the values in this arrayref
• Returns: Grinder::KmerCollection object 🫶

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🍓 k

• Usage: $col->k;
• Function: Get the length of the kmers
• Args: None
• Returns: Positive integer 🔢

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💜 weights

• Usage: $col->weights({'seq1' => 3, 'seq10' => 0.45});
• Function: Get or set the weight of each sequence. Each sequence is given a weight of 1 by default.
• Args: hashref where the keys are sequence IDs and the values are the weight of the corresponding (e.g. their relative abundance)
• Returns: Grinder::KmerCollection object

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🌈 collection_by_kmer

• Usage: $col->collection_by_kmer;
• Function: Get the collection of kmers, indexed by kmer
• Args: None
• Returns: A hashref of hashref of arrayref:

hash->{kmer}->{ID of sequences with this kmer}->[starts of kmer on sequence]

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🌸 collection_by_seq

• Usage: $col->collection_by_seq;
• Function: Get the collection of kmers, indexed by sequence ID
• Args: None
• Returns: A hashref of hashref of arrayref:

hash->{ID of sequences with this kmer}->{kmer}->[starts of kmer on sequence]

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🎀 add_file

• Usage: $col->add_file('seqs.fa');
• Function: Process the kmers in the given file of sequences.
• Args: filename
• Returns: Grinder::KmerCollection object

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✨ add_seqs

• Usage: $col->add_seqs([$seq1, $seq2]);
• Function: Process the kmers in the given sequences.
• Args:
  • arrayref of Bio::Seq or Bio::SeqFeature objects
  • arrayref of IDs to use for the indexing of the sequences
• Returns: Grinder::KmerCollection object

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🔥 filter_rare

• Usage: $col->filter_rare( 2 );
• Function: Remove kmers occurring at less than the (weighted) abundance specified
• Args: integer
• Returns: Grinder::KmerCollection object

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💖 filter_shared

• Usage: $col->filter_shared( 2 );
• Function: Remove kmers occurring in less than the number of sequences specified
• Args: integer
• Returns: Grinder::KmerCollection object

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⭐ counts

• Usage: $col->counts
• Function: Calculate the total count of each kmer. Counts are affected by the weights given to the sequences.
• Args:
  • restrict sequences to search to specified sequence ID (optional)
  • starting position from which counting should start (optional)
  • 0 to report counts (default), 1 to report frequencies (normalize to 1)
• Returns:
  • arrayref of the different kmers
  • arrayref of the corresponding total counts

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🦋 sources

• Usage: $col->sources()
• Function: Return the sources of a kmer and their (weighted) abundance.
• Args:
  • kmer to get the sources of
  • sources to exclude from the results (optional)
  • 0 to report counts (default), 1 to report frequencies (normalize to 1)
• Returns:
  • arrayref of the different sources
  • arrayref of the corresponding total counts

If the kmer requested does not exist, the array will be empty. 😭

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💅 kmers

• Usage: $col->kmers('seq1');
• Function: This is the inverse of sources(). Return the kmers found in a sequence (given its ID) and their (weighted) abundance.
• Args:
  • sequence ID to get the kmers of
  • 0 to report counts (default), 1 to report frequencies (normalize to 1)
• Returns:
  • arrayref of sequence IDs
  • arrayref of the corresponding total counts

If the sequence ID requested does not exist, the arrays will be empty. 😭

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🧚 positions

• Usage: $col->positions()
• Function: Return the positions of the given kmer on a given sequence. An error is reported if the kmer requested does not exist — like, it will straight up tell you, no hiding it 💀
• Args:
  • desired kmer
  • desired sequence with this kmer
• Returns: Arrayref of the different positions. The arrays will be empty if the desired combination of kmer and sequence was not found.

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okay bestie that's the whole page, you ate it, go forth and count your kmers 🫶🌸

perl v5.32.0 · 2020-12-03 · Grinde...lection(3pm) — and that's the footer, periodt. 💖✨