NAME

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

SYNOPSIS

  # 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;
  }

  # 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

Boulder::Unigene provides retrieval and parsing services for NCBI Unigene records. It returns Unigene entries in Stone format, allowing easy access to the various fields and values. Boulder::Unigene is a descendent of Boulder::Stream, and provides a stream-like interface to a series of Stone objects.

Access to Unigene is provided by one accessors, which give access to 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 accessors is:

File: This provides access to local Unigene 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 Unigene entry from a text string stored in a scalar variable, returning a Stone object.

Boulder::Unigene methods

This section lists the public methods that the Boulder::Unigene class makes available.

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 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 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.

put()

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::Unigene object back into Unigene 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 Unigene entry.

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.

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 ???

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

AUTHOR

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

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.