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

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.