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::Medline(3pm) User Contributed Perl Documentation Boulder::Medline(3pm) NAME
Boulder::Medline - Fetch Medline data records as parsed Boulder Stones SYNOPSIS
# parse a file of Medline records $ml = new Boulder::Medline(-accessor=>'File', -param => '/data/medline/medline.txt'); while (my $s = $ml->get) { print $s->Identifier; print $s->Abstract; } # parse flatfile yourself open (ML,"/data/medline/medline.txt"); local $/ = "*RECORD*"; while (<ML>) { my $s = Boulder::Medline->parse($_); # etc. } DESCRIPTION
Boulder::Medline provides retrieval and parsing services for Medline records Boulder::Medline provides retrieval and parsing services for NCBI Medline records. It returns Medline entries in Stone format, allowing easy access to the various fields and values. Boulder::Medline is a descendent of Boulder::Stream, and provides a stream-like interface to a series of Stone objects. Access to Medline is provided by one accessors, which give access to local Medline database. When you create a new Boulder::Medline 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 Medline entries by reading from a flat file. 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 Medline entry from a text string stored in a scalar variable, returning a Stone object. Boulder::Medline methods This section lists the public methods that the Boulder::Medline class makes available. new() # Local fetch via File $ml=new Boulder::Medline(-accessor => 'File', -param => '/data/medline/medline.txt'); The new() method creates a new Boulder::Medline 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 Medline entries from. get() The get() method is inherited from Boulder::Stream, and simply returns the next parsed Medline 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::Medline object back into Medline flatfile form. OUTPUT TAGS
The tags returned by the parsing operation are taken from the MEDLARS definition file MEDDOC.DOC Top-Level Tags These are tags that appear at the top level of the parsed Medline entry. ABSTRACT ABSTRACT AUTHOR ADDRESS AUTHOR CALL NUMBER CAS REGISTRY/EC NUMBER CLASS UPDATE DATE COMMENTS COUNTRY DATE OF ENTRY DATE OF PUBLICATION ENGLISH ABSTRACT INDICATOR ENTRY MONTH GENE SYMBOL ID NUMBER INDEXING PRIORITY ISSN ISSUE/PART/SUPPLEMENT JOURNAL SUBSET JOURNAL TITLE CODE LANGUAGE LAST REVISION DATE MACHINE-READABLE IDENTIFIER MeSH HEADING NO-AUTHOR INDICATOR NOT FOR PUBLICATION NUMBER OF REFERENCES PAGINATION PERSONAL NAME AS SUBJECT PUBLICATION TYPE RECORD ORIGINATOR SECONDARY SOURCE ID SPECIAL LIST INDICATOR TITLE TITLE ABBREVIATION TRANSLITERATED/VERNACULAR TITLE UNIQUE IDENTIFIER VOLUME ISSUE Identifier The Medline identifier of this entry. Identifier is a single-value tag. Example: my $identifierNo = $s->Identifier; Title The Medline title for this entry. Example: my $titledef=$s->Title; 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 2011-03-05 Boulder::Medline(3pm)