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Boulder::LocusLink(3pm) User Contributed Perl Documentation Boulder::LocusLink(3pm)

NAME

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

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

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.

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.

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.

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;

SEE ALSO

Boulder, Boulder::Blast, Boulder::Genbank

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.

2022-06-08 perl v5.34.0