Boulder::Unigene(3pm)

🦋 Boulder::Unigene — the perl page, but make it cute

okay bestie, welcome to the Boulder::Unigene manual page (that's the Boulder::Unigene(3pm) one, from User Contributed Perl Documentation 💖). Sit down, hydrate, and let's get into it — this is the module that goes and grabs your Unigene records and hands them back to you as parsed Boulder Stones. no cap.

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✨ NAME ✨

Boulder::Unigene — Fetch Unigene data records as parsed Boulder Stones 🎀

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🌸 SYNOPSIS 🌸

two ways to do the thing, bestie. first: let it parse a file for you.

# parse a file of Unigene records
$ug = new Boulder::Unigene(-accessor=>'File',
                           -param => '/data/unigene/Hs.dat');
while (my $s = $ug->get) {
  print $s->Identifier;
  print $s->Gene;
}

second: you do the flatfile wrangling yourself, main character energy.

# parse flatfile records yourself
open (UG,"/data/unigene/Hs.dat");
local $/ = "*RECORD*";
while (<UG>) {
   my $s = Boulder::Unigene->parse($_);
   # etc.
}

---

💅 DESCRIPTION 💅

Boulder::Unigene provides retrieval and parsing services for UNIGENE records — and also, more specifically, for NCBI Unigene records. It hands you back Unigene entries in Stone format, so all the various fields and values are just… there. easy access, slay. And plot twist: Boulder::Unigene is a descendent of Boulder::Stream, so it gives you a stream-like interface over a whole series of Stone objects. it's giving inheritance, it's giving legacy. 👑

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

• File — this gives you access to local Unigene entries by reading from a flat file (typically the Hs.dat file you can download from NCBI's Ftp site). The stream returns a Stone for 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. 🍓

Oh and also — it is also possible to parse a single Unigene entry from a text string stored in a scalar variable, returning a Stone object. little bonus, we love that for us.

🫶 Boulder::Unigene methods

This section lists the public methods that the Boulder::Unigene class makes available. yes bestie, here's the menu.

• new()

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

The new() method creates a new Boulder::Unigene stream on the accessor provided. The only possible accessor is File. If it goes well, the method returns the stream object. Otherwise it returns undef — and we do NOT love that, but that's the deal. 😭

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 you don't specify it, it defaults to File.

-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 Unigene entries from.

• get() — the get() method is inherited from Boulder::Stream, and simply returns the next parsed Unigene 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. iconic behaviour honestly.
• 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: it is currently not possible to write a Boulder::Unigene object back into Unigene 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. so we work with what we've got, fr fr.

⭐ Top-Level Tags

These are tags that appear at the top level of the parsed Unigene entry. the VIP section.

• Identifier — the Unigene identifier of this entry. Identifier is a single-value tag.

Example:

      my $identifierNo = $s->Identifier;

• Title — the Unigene title for this entry.

Example:

      my $titledef=$s->Title;

• Gene — the Gene associated with this Unigene entry

Example:

      my $thegene=$s->Gene;

• Cytoband — the cytological band position of this entry

Example:

      my $thecytoband=$s->Cytoband;

• Counts — the number of EST in this record

Example:

      my $thecounts=$s->Counts;

• LocusLink — the id of the LocusLink entry associated with this record

Example:

      my $thelocuslink=$s->LocusLink;

• Chromosome — this field contains a list, of the chromosomes numbers in which this entry has been linked

Example:

      my @theChromosome=$s->Chromosome;

🧚 STS

Multiple records in the form ^STS ACC=XXXXXX NAME=YYYYYY

• ACC
• NAME

💜 TXMAP

Multiple records in the form ^TXMAP XXXXXXX; MARKER=YYYYY; RHPANEL=ZZZZ

The TXMAP tag points to a Stone record that contains multiple subtags. Each subtag is the name of a feature which points, in turn, to a Stone that describes the feature's location and other attributes. nested Stones, we're going deeper, obsessed. 🌀

Each feature will contain one or more of the following subtags:

• MARKER
• RHPANEL

🔥 PROTSIM

Multiple records in the form ^PROTSIM ORG=XXX; PROTID=DBID:YYY; PCT=ZZZ; ALN=QQQQ

Where DBID is PID for indicate presence of GenPept identifier, SP to indicate SWISSPROT identifier, PIR to indicate PIR identifier, PRF to indicate ??? (yes, the original really says ???, and honestly, mood.)

• ORG
• PROTID
• PCT
• ALN

👑 SEQUENCE

Multiple records in the form ^SEQUENCE ACC=XXX; NID=YYYY; PID = CLONE= END= LID=

• ACC
• NID
• PID
• CLONE
• END
• LID

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🌸 SEE ALSO 🌸

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

go read those too, they're the friend group. 🫶

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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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okay that's the whole page bestie, no notes. this was perl v5.34.0, dated 2022-06-08, and it's the Boulder::Unigene(3pm) page — love that for us, go parse something iconic. ✨🦋🎀