stone::gb_sequence(3pm) [debian man page]
Stone::GB_Sequence(3pm) User Contributed Perl Documentation Stone::GB_Sequence(3pm) NAME
Stone::GB_Sequence - Specialized Access to GenBank Records SYNOPSIS
use Boulder::Genbank; # No need to use Stone::GB_Sequence directly $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028); while ($entry = <$gb>) { print "Entry's length is ",$entry->length," "; @cds = $entry->match_features(-type=>'CDS'); @exons = $entry->match_features(-type=>'Exon',-start=>100,-end=>300); } } DESCRIPTION
Stone::GB_Sequence provides several specialized access methods to the various fields in a GenBank flat file record. You can return the sequence as a Bio::Seq object, or query the sequence for features that match positional or descriptional criteria that you provide. CONSTRUCTORS
This class is not intended to be created directly, but via a Boulder::Genbank stream. METHODS
In addition to the standard Stone methods and accessors, the following methods are provided. In the synopses, the variable $entry refers to a previously-created Stone::GB_Sequence object. $length = $entry->length Get the length of the sequence. $start = $entry->start Get the start position of the sequence, currently always "1". $end = $entry->end Get the end position of the sequence, currently always the same as the length. @feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon']) features() will search the entry feature list for those features that meet certain criteria. The criteria are specified using the -pos and/or -type argument names, as shown below. -pos Provide a position or range of positions which the feature must overlap. A single position is specified in this way: -pos => 1500; # feature must overlap postion 1500 or a range of positions in this way: -pos => [1000,1500]; # 1000 to 1500 inclusive If no criteria are provided, then features() returns all the features, and is equivalent to calling the Features() accessor. -type, -types Filter the list of features by type or a set of types. Matches are case-insensitive, so "exon", "Exon" and "EXON" are all equivalent. You may call with a single type as in: -type => 'Exon' or with a list of types, as in -types => ['Exon','CDS'] The names "-type" and "-types" can be used interchangeably. $seqObj = $entry->bioSeq; Returns a Bio::Seq object from the Bioperl project. Dies with an error message unless the Bio::Seq module is installed. AUTHOR
Lincoln D. Stein <lstein@cshl.org>. COPYRIGHT
Copyright 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor NY. This module can be used and distributed on the same terms as Perl itself. SEE ALSO
Boulder, <Boulder:Genbank>, Stone perl v5.10.1 2011-03-05 Stone::GB_Sequence(3pm)
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Boulder::LocusLink(3pm) User Contributed Perl Documentation Boulder::LocusLink(3pm) NAME
Boulder::LocusLink - Fetch LocusLink data records as parsed Boulder Stones SYNOPSIS
# 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. } DESCRIPTION
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::LocusLink methods 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. 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 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 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. perl v5.10.1 2004-01-09 Boulder::LocusLink(3pm)