bionic (3) Boulder::Unigene.3pm.gz

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.