Boulder::LocusLink - Fetch LocusLink 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::LocusLink(3pm)

       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:

       File
         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.

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

       new()
              # 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.

       get()
           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.

       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::LocusLink object back into LocusLink flatfile form.

       Boulder::LocusLink - Fetch LocusLink 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 LocusLink entry.

       Identifier
           The LocusLink identifier of this entry.  Identifier is a single-value tag.

           Example:

                 my $identifierNo = $s->Identifier;

       Current_locusid
           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;

       Organism Source species ased on NCBI's Taxonomy
           Example:
                 my $theorganism=$s->Organism;

       Status Type of reference sequence record. If "PROVISIONAL" then means that is generated automatically
       from existing Genbank record and information stored in the LocusLink database, no curation. If "REVIEWED"
       than it means that is generated from the most representative complete GenBank sequence or merge of
       GenBank sequenes and from information stored in the LocusLink database
           Example:
                 my $thestatus=$s->Status;

       LocAss Here comes a complex record ... made up of LOCUS_STRING, NM         The value in the LOCUS field
       of the RefSeq record , NP         The RefSeq accession number for an mRNA record, PRODUCT    The name of
       the produc tof this transcript, TRANSVAR   a variant-specific description, ASSEMBLY   The Genbank
       accession used to assemble the refseq record
           Example:
                 my $theprod=$s->LocAss->Product;

       AccProt Here comes a complex record ... made up of ACCNUM        Nucleotide sequence accessio number TYPE
       e=EST, m=mRNA, g=Genomic PROT         set of PID values for the coding region or regions annotated on the
       nucleotide record. The first value is the PID (an integer or null), then either MMDB or na, separated
       from the PID by a |. If MMDB is present, it indicates there are structur edata available for a protein
       related to the protein referenced by the PID Example: my $theprot=$s->AccProt->Prot;
       OFFICIAL_SYMBOL The symbol used for gene reports, validated by the appropriate nomenclature committee
       PREFERRED_SYMBOL Interim symbol used for display
       OFFICIAL_GENE_NAME The gene description used for gene reports validate by the appropriate nomenclatur
       eommittee. If the symbol is official, the gene name will be official. No records will have both official
       and interim nomenclature.
       PREFERRED_GENE_NAME Interim used for display
       PREFERRED_PRODUCT The name of the product used in the RefSeq record
       ALIAS_SYMBOL Other symbols associated with this gene
       ALIAS_PROT Other protein names associated with this gene
       PhenoTable A complex record made up of Phenotype Phenotype_ID
       SUmmary
       Unigene
       Omim
       Chr
       Map
       STS
       ECNUM
       ButTable BUTTON LINK
       DBTable DB_DESCR DB_LINK
       PMID a subset of publications associated with this locus with the link being the PubMed unique identifier
       comma separated

       Boulder, Boulder::Blast, Boulder::Genbank

         # 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.
         }