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

       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.

perl v5.34.0                                       2022-06-08                              Boulder::Unigene(3pm)

       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::Unigenemethods
       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.

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

       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-LevelTags
       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;

   STSMultiplerecordsintheform^STSACC=XXXXXXNAME=YYYYYY
       ACC
       NAME

   TXMAPMultiplerecordsintheform^TXMAPXXXXXXX;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

   PROTSIMMultiplerecordsintheform^PROTSIMORG=XXX;PROTID=DBID:YYY;PCT=ZZZ;ALN=QQQQWhereDBIDisPIDforindicatepresenceofGenPeptidentifier,SPtoindicateSWISSPROTidentifier,PIRtoindicatePIRidentifier,PRFtoindicate???
       ORG
       PROTID
       PCT
       ALN

   SEQUENCEMultiplerecordsintheform^SEQUENCEACC=XXX;NID=YYYY;PID=CLONE=END=LID=
       ACC
       NID
       PID
       CLONE
       END
       LID

       Boulder, Boulder::Blast, Boulder::Genbank

         # 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.
         }