Boulder::Unigene(3) User Contributed Perl Documentation Boulder::Unigene(3)NAMEBoulder::Unigene - Fetch Unigene data records as parsed Boulder Stones
SYNOPSIS
# parse a file of Unigene records
$ug = new Boulder::Unigene(-accessor=>'File',
-param => '/data/unigene/Hs.dat');
while (my $s = $ug->get) {
print $s->Identifier;
print $s->Gene;
}
# parse flatfile records yourself
open (UG,"/data/unigene/Hs.dat");
local $/ = "*RECORD*";
while (<UG>) {
my $s = Boulder::Unigene->parse($_);
# etc.
}
DESCRIPTIONBoulder::Unigene provides retrieval and parsing services for UNIGENE
records
Boulder::Unigene provides retrieval and parsing services for NCBI
Unigene records. It returns Unigene entries in Stone format, allowing
easy access to the various fields and values. Boulder::Unigene is a
descendent of Boulder::Stream, and provides a stream-like interface to
a series of Stone objects.
Access to Unigene is provided by one accessors, which give access to
local Unigene database. When you create a new Boulder::Unigene 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 Unigene 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 Unigene entry from a text string
stored in a scalar variable, returning a Stone object.
Boulder::Unigene methods
This section lists the public methods that the Boulder::Unigene class
makes available.
new()
# Local fetch via File
$ug=new Boulder::Unigene(-accessor => 'File',
-param => '/data/unigene/Hs.dat');
The new() method creates a new Boulder::Unigene 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 Unigene
entries from.
get()
The get() method is inherited from Boulder::Stream, and simply
returns the next parsed Unigene 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::Unigene object back into Unigene 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 Unigene
entry.
Identifier
The Unigene identifier of this entry. Identifier is a single-value
tag.
Example:
my $identifierNo = $s->Identifier;
Title
The Unigene title for this entry.
Example:
my $titledef=$s->Title;
Gene The Gene associated with this Unigene entry
Example:
my $thegene=$s->Gene;
Cytoband The cytological band position of this entry
Example:
my $thecytoband=$s->Cytoband;
Counts The number of EST in this record
Example:
my $thecounts=$s->Counts;
LocusLink The id of the LocusLink entry associated with this record
Example:
my $thelocuslink=$s->LocusLink;
Chromosome This field contains a list, of the chromosomes numbers in
which this entry has been linked
Example:
my @theChromosome=$s->Chromosome;
STS Multiple records in the form ^STS ACC=XXXXXX NAME=YYYYYY
ACC
NAME
TXMAP Multiple records in the form ^TXMAP XXXXXXX; MARKER=YYYYY;
RHPANEL=ZZZZ
The TXMAP tag points to a Stone record that contains multiple subtags.
Each subtag is the name of a feature which points, in turn, to a Stone
that describes the feature's location and other attributes.
Each feature will contain one or more of the following subtags:
MARKER
RHPANEL
PROTSIM Multiple records in the form ^PROTSIM ORG=XXX; PROTID=DBID:YYY;
PCT=ZZZ; ALN=QQQQ Where DBID is PID for indicate presence of GenPept
identifier, SP to indicate SWISSPROT identifier, PIR to indicate PIR
identifier, PRF to indicate ???
ORG
PROTID
PCT
ALN
SEQUENCE Multiple records in the form ^SEQUENCE ACC=XXX; NID=YYYY; PID =
CLONE= END= LID=
ACC
NID
PID
CLONE
END
LID
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 v5.14.1 2000-01-18 Boulder::Unigene(3)
