Boulde...usLink(3pm)

✨ NAME ✨

Boulder::LocusLink — bestie, this one fetches LocusLink data records and hands them back to you as parsed Boulder Stones. That's it, that's the whole job. 🪨💖

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🌈 SYNOPSIS 🌈

# parse a file of LocusLink records
$ll = new Boulder::LocusLink(-accessor=>'File',
                           -param => '/home/data/LocusLink/LL_tmpl');
while (my $s = $ll->get) {
  print $s->Identifier;
  print $s->Gene;
}

# parse flatfile records yourself
open (LL,"/home/data/LocusLink/LL_tmpl");
local $/ = "*RECORD*";
while (<LL>) {
   my $s = Boulder::LocusLink->parse($_);
   # etc.
}

---

💅 DESCRIPTION 💅

okay so. Boulder::LocusLink provides retrieval and parsing services for LocusLink records. 🫶

And like, more specifically: Boulder::LocusLink provides retrieval and parsing services for NCBI LocusLink records. It returns Unigene entries in Stone format, which is the whole point, because that gives you easy access to the various fields and values. Also Boulder::LocusLink is a descendent of Boulder::Stream, and it gives you a stream-like interface to a series of Stone objects. Iconic inheritance moment, honestly. 👑

Access to LocusLink is provided by one accessors, which give access to the local LocusLink database. When you create a new Boulder::LocusLink stream, you provide the accessors, along with accessor-specific parameters that control what entries to fetch. The accessors is:

• File — this provides access to local LocusLink entries by reading from a flat file (typically the Hs.dat file downloadable from NCBI's Ftp site). The stream will return a Stone corresponding to each of the entries in the file, starting from the top of the file and working downward. The parameter is the path to the local file. 🍓

It is also possible to parse a single LocusLink entry from a text string stored in a scalar variable, returning a Stone object. cute, right? 💖

🧚 Boulder::LocusLink methods 🧚

This section lists the public methods that the Boulder::LocusLink class makes available. Get comfy.

new()

# Local fetch via File
$ug=new Boulder::LocusLink(-accessor  =>  'File',
                         -param     =>  '/data/LocusLink/Hs.dat');

The new() method creates a new Boulder::LocusLink stream on the accessor provided. The only possible accessors is File. If it goes well, the method returns the stream object. Otherwise it returns undef. 😭

new() takes the following arguments:

        -accessor       Name of the accessor to use
        -param          Parameters to pass to the accessor

Specify the accessor to use with the -accessor argument. If not specified, it defaults to File. (defaults are self-care fr fr 🌸)

-param is an accessor-specific argument. The possibilities is:

• For File, the -param argument must point to a string-valued scalar, which will be interpreted as the path to the file to read LocusLink entries from.

get()

The get() method is inherited from Boulder::Stream, and simply returns the next parsed LocusLink Stone, or undef if there is nothing more to fetch. It has the same semantics as the parent class, including the ability to restrict access to certain top-level tags. 👑

put()

The put() method is inherited from the parent Boulder::Stream class, and will write the passed Stone to standard output in Boulder format. Which means — and I need you to hear me on this — it is currently not possible to write a Boulder::LocusLink object back into LocusLink flatfile form. One-way street, bestie. 💀

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🎀 OUTPUT TAGS 🎀

The tags returned by the parsing operation are taken from the names shown in the Flat file Hs.dat, since no better description of them is provided yet by the database source producer. We work with what we got. 🙈

⭐ Top-Level Tags ⭐

These are tags that appear at the top level of the parsed LocusLink entry.

• Identifier — The LocusLink identifier of this entry. Identifier is a single-value tag.

Example:

      my $identifierNo = $s->Identifier;

• Current_locusid — If a locus has been merged with another, the Current_locusid contains the previous LOCUSID line (a bit confusing, shall be called "previous_locusid", but this is defined in NCBI README File ... 😭).

Example:

      my $prevlocusid=$s->Current_locusid;

• Organism — Source species, based on NCBI's Taxonomy.

Example:

      my $theorganism=$s->Organism;

• Status — Type of reference sequence record. If "PROVISIONAL" then that means it is generated automatically from an existing Genbank record and information stored in the LocusLink database, no curation. If "REVIEWED" then it means that it is generated from the most representative complete GenBank sequence or merge of GenBank sequences and from information stored in the LocusLink database.

Example:

      my $thestatus=$s->Status;

• LocAss — here comes a complex record ... made up of:
  • LOCUS_STRING
  • NM — the value in the LOCUS field of the RefSeq record
  • NP — the RefSeq accession number for an mRNA record
  • PRODUCT — the name of the product of this transcript
  • TRANSVAR — a variant-specific description
  • ASSEMBLY — the Genbank accession used to assemble the refseq record

Example:

      my $theprod=$s->LocAss->Product;

• AccProt — here comes a complex record ... made up of:
  • ACCNUM — nucleotide sequence accession number
  • TYPE — e=EST, m=mRNA, g=Genomic
  • PROT — set of PID values for the coding region or regions annotated on the nucleotide record. The first value is the PID (an integer or null), then either MMDB or na, separated from the PID by a |. If MMDB is present, it indicates there are structure data available for a protein related to the protein referenced by the PID.

Example: my $theprot=$s->AccProt->Prot;

• OFFICIAL_SYMBOL — The symbol used for gene reports, validated by the appropriate nomenclature committee.
• PREFERRED_SYMBOL — Interim symbol used for display.
• OFFICIAL_GENE_NAME — The gene description used for gene reports, validated by the appropriate nomenclature committee. If the symbol is official, the gene name will be official. No records will have both official and interim nomenclature.
• PREFERRED_GENE_NAME — Interim, used for display.
• PREFERRED_PRODUCT — The name of the product used in the RefSeq record.
• ALIAS_SYMBOL — Other symbols associated with this gene.
• ALIAS_PROT — Other protein names associated with this gene.
• PhenoTable — A complex record made up of Phenotype, Phenotype_ID, SUmmary.
• Unigene
• Omim
• Chr
• Map
• STS
• ECNUM
• ButTable — BUTTON LINK
• DBTable — DB_DESCR, DB_LINK
• PMID — a subset of publications associated with this locus, with the link being the PubMed unique identifier, comma separated.

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💜 SEE ALSO 💜

• Boulder
• Boulder::Blast
• Boulder::Genbank

go read those too bestie, iykyk 📚✨

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👑 AUTHOR 👑

Lincoln Stein <lstein@cshl.org>. Luca I.G. Toldo <luca.toldo@merck.de>

Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

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k that's the whole page bestie, go forth and parse 💖✨

This lil doc shipped with perl v5.34.0, dated 2022-06-08, from the User Contributed Perl Documentation collection. slay, stay hydrated, and always read your README files 🫶🌈