1Boulder::LocusLink(3) User Contributed Perl DocumentationBoulder::LocusLink(3)
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NAME

6       Boulder::LocusLink - Fetch LocusLink data records as parsed Boulder
7       Stones
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SYNOPSIS

10         # parse a file of LocusLink records
11         $ll = new Boulder::LocusLink(-accessor=>'File',
12                                    -param => '/home/data/LocusLink/LL_tmpl');
13         while (my $s = $ll->get) {
14           print $s->Identifier;
15           print $s->Gene;
16         }
17
18         # parse flatfile records yourself
19         open (LL,"/home/data/LocusLink/LL_tmpl");
20         local $/ = "*RECORD*";
21         while (<LL>) {
22            my $s = Boulder::LocusLink->parse($_);
23            # etc.
24         }
25

DESCRIPTION

27       Boulder::LocusLink provides retrieval and parsing services for
28       LocusLink records
29
30       Boulder::LocusLink provides retrieval and parsing services for NCBI
31       LocusLink records.  It returns Unigene entries in Stone format,
32       allowing easy access to the various fields and values.
33       Boulder::LocusLink is a descendent of Boulder::Stream, and provides a
34       stream-like interface to a series of Stone objects.
35
36       Access to LocusLink is provided by one accessors, which give access to
37       local LocusLink database.  When you create a new Boulder::LocusLink
38       stream, you provide the accessors, along with accessor-specific
39       parameters that control what entries to fetch.  The accessors is:
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41       File
42         This provides access to local LocusLink entries by reading from a
43         flat file (typically Hs.dat file downloadable from NCBI's Ftp site).
44         The stream will return a Stone corresponding to each of the entries
45         in the file, starting from the top of the file and working downward.
46         The parameter is the path to the local file.
47
48       It is also possible to parse a single LocusLink entry from a text
49       string stored in a scalar variable, returning a Stone object.
50
51   Boulder::LocusLink methods
52       This section lists the public methods that the Boulder::LocusLink class
53       makes available.
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55       new()
56              # Local fetch via File
57              $ug=new Boulder::LocusLink(-accessor  =>  'File',
58                                       -param     =>  '/data/LocusLink/Hs.dat');
59
60           The new() method creates a new Boulder::LocusLink stream on the
61           accessor provided.  The only possible accessors is File.  If
62           successful, the method returns the stream object.  Otherwise it
63           returns undef.
64
65           new() takes the following arguments:
66
67                   -accessor       Name of the accessor to use
68                   -param          Parameters to pass to the accessor
69
70           Specify the accessor to use with the -accessor argument.  If not
71           specified, it defaults to File.
72
73           -param is an accessor-specific argument.  The possibilities is:
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75           For File, the -param argument must point to a string-valued scalar,
76           which will be interpreted as the path to the file to read LocusLink
77           entries from.
78
79       get()
80           The get() method is inherited from Boulder::Stream, and simply
81           returns the next parsed LocusLink Stone, or undef if there is
82           nothing more to fetch.  It has the same semantics as the parent
83           class, including the ability to restrict access to certain top-
84           level tags.
85
86       put()
87           The put() method is inherited from the parent Boulder::Stream
88           class, and will write the passed Stone to standard output in
89           Boulder format.  This means that it is currently not possible to
90           write a Boulder::LocusLink object back into LocusLink flatfile
91           form.
92

OUTPUT TAGS

94       The tags returned by the parsing operation are taken from the names
95       shown in the Flat file Hs.dat since no better description of them is
96       provided yet by the database source producer.
97
98   Top-Level Tags
99       These are tags that appear at the top level of the parsed LocusLink
100       entry.
101
102       Identifier
103           The LocusLink identifier of this entry.  Identifier is a single-
104           value tag.
105
106           Example:
107
108                 my $identifierNo = $s->Identifier;
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110       Current_locusid
111           If a locus has been merged with another, the Current_locusid
112           contains the previous LOCUSID line (A bit confusing, shall be
113           called "previous_locusid", but this is defined in NCBI README File
114           ... ).
115
116           Example:
117                 my $prevlocusid=$s->Current_locusid;
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119       Organism Source species ased on NCBI's Taxonomy
120           Example:
121                 my $theorganism=$s->Organism;
122
123       Status Type of reference sequence record. If "PROVISIONAL" then means
124       that is generated automatically from existing Genbank record and
125       information stored in the LocusLink database, no curation. If
126       "REVIEWED" than it means that is generated from the most representative
127       complete GenBank sequence or merge of GenBank sequenes and from
128       information stored in the LocusLink database
129           Example:
130                 my $thestatus=$s->Status;
131
132       LocAss Here comes a complex record ... made up of LOCUS_STRING, NM
133       The value in the LOCUS field of the RefSeq record , NP         The
134       RefSeq accession number for an mRNA record, PRODUCT    The name of the
135       produc tof this transcript, TRANSVAR   a variant-specific description,
136       ASSEMBLY   The Genbank accession used to assemble the refseq record
137           Example:
138                 my $theprod=$s->LocAss->Product;
139
140       AccProt Here comes a complex record ... made up of ACCNUM
141       Nucleotide sequence accessio number TYPE         e=EST, m=mRNA,
142       g=Genomic PROT         set of PID values for the coding region or
143       regions annotated on the nucleotide record. The first value is the PID
144       (an integer or null), then either MMDB or na, separated from the PID by
145       a |. If MMDB is present, it indicates there are structur edata
146       available for a protein related to the protein referenced by the PID
147       Example: my $theprot=$s->AccProt->Prot;
148       OFFICIAL_SYMBOL The symbol used for gene reports, validated by the
149       appropriate nomenclature committee
150       PREFERRED_SYMBOL Interim symbol used for display
151       OFFICIAL_GENE_NAME The gene description used for gene reports validate
152       by the appropriate nomenclatur eommittee. If the symbol is official,
153       the gene name will be official. No records will have both official and
154       interim nomenclature.
155       PREFERRED_GENE_NAME Interim used for display
156       PREFERRED_PRODUCT The name of the product used in the RefSeq record
157       ALIAS_SYMBOL Other symbols associated with this gene
158       ALIAS_PROT Other protein names associated with this gene
159       PhenoTable A complex record made up of Phenotype Phenotype_ID
160       SUmmary
161       Unigene
162       Omim
163       Chr
164       Map
165       STS
166       ECNUM
167       ButTable BUTTON LINK
168       DBTable DB_DESCR DB_LINK
169       PMID a subset of publications associated with this locus with the link
170       being the PubMed unique identifier comma separated
171

SEE ALSO

173       Boulder, Boulder::Blast, Boulder::Genbank
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AUTHOR

176       Lincoln Stein <lstein@cshl.org>.  Luca I.G. Toldo <luca.toldo@merck.de>
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178       Copyright (c) 1997 Lincoln D. Stein Copyright (c) 1999 Luca I.G. Toldo
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180       This library is free software; you can redistribute it and/or modify it
181       under the same terms as Perl itself.  See DISCLAIMER.txt for
182       disclaimers of warranty.
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186perl v5.38.0                      2023-07-20             Boulder::LocusLink(3)
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