---
name: "Boulder::LocusLink"
section: "3"
platform: "linux"
package: "libboulder-perl"
version: "1.30-1"
release: "Debian 3.1 (Sarge)"
platforms: ["linux"]
url: "https://new.carta.tech/Boulder::LocusLink"
---

# Boulder::LocusLink(3)

Boulder::LocusLink - Fetch LocusLink data records as parsed Boulder Stones

```
  # 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.
  }
```

Boulder::LocusLink provides retrieval and parsing services for LocusLink records Boulder::LocusLink provides retrieval and parsing services for NCBI LocusLink records.  It returns Unigene entries in Stone format, allowing easy access to the various fields and values. Boulder::LocusLink is a descendent of Boulder::Stream, and provides a stream-like interface to a series of Stone objects. Access to LocusLink is provided by one *accessors*, which give access to  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: This provides access to local LocusLink entries by reading from a flat file (typically 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.\
 **Boulder::LocusLink methods** This section lists the public methods that the *Boulder::LocusLink* class makes available.

```
   # 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 successful, 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**.

**-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. 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. The *put()* method is inherited from the parent Boulder::Stream class, and will write the passed Stone to standard output in Boulder format. This means that it is currently not possible to write a Boulder::LocusLink object back into LocusLink flatfile form. 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.\
 **Top-Level Tags** These are tags that appear at the top level of the parsed LocusLink entry. The LocusLink identifier of this entry.  Identifier is a single-value tag.

Example:

```
      my $identifierNo = $s->Identifier;
```

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; Example:\
       my `$theorganism`=$s-\>Organism; Example:\
       my `$thestatus`=$s-\>Status; Example:\
       my `$theprod`=$s-\>LocAss-\>Product; Boulder, Boulder::Blast, Boulder::Genbank 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.