Boulder::Blast::WU(3pm) User Contributed Perl Documentation Boulder::Blast::WU(3pm)NAME
Boulder::Blast::WU - Parse and read WU-BLAST files
SYNOPSIS
Not for direct use. Use Boulder::Blast instead.
DESCRIPTION
Specialized parser for WUBLAST format BLAST output. Loaded automatically by Boulder::Blast.
SEE ALSO
Boulder, Boulder::GenBank, Boulder::Blast
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 1998 Cold Spring Harbor Laboratory
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 2000-06-08 Boulder::Blast::WU(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)