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::XML(3pm) User Contributed Perl Documentation Boulder::XML(3pm)NAME
Boulder::XML - XML format input/output for Boulder streams
SYNOPSIS
use Boulder::XML;
$stream = Boulder::XML->newFh;
while ($stone = <$stream>) {
print $stream $stone;
}
DESCRIPTION
Boulder::XML generates BoulderIO streams from XML files and/or streams. It is also able to output Boulder Stones in XML format. Its
semantics are similar to those of Boulder::Stream, except that there is never any pass-through behavior.
Because XML was not designed for streaming, some care must be taken when reading an XML document into a series of Stones. Consider this
XML document:
<?xml version="1.0" standalone="yes"?>
<Paper>
<Author>Lincoln Stein</Author>
<Author>Jean Siao</Author>
<Date>September 29, 1999</Date>
<Copyright copyrighted="yes">1999 Lincoln Stein</Copright>
<Abstract>
This is the abstract. It is not anything very fancy,
but it will do.
</Abstract>
<Citation>
<Author>Fitchberg J</Author>
<Journal>Journal of Irreproducible Results</Journal>
<Volume>23</Volume>
<Year>1998</Volume>
</Citation>
<Citation>
<Author>Clemenson V</Author>
<Journal>Ecumenica</Journal>
<Volume>10</Volume>
<Year>1968</Volume>
</Citation>
<Citation>
<Author>Ruggles M</Author>
<Journal>Journal of Aesthetic Surgery</Journal>
<Volume>10</Volume>
<Year>1999</Volume>
</Citation>
</Paper>
Ordinarily the document will be construed as a single Paper tag containing subtags Author, Date, Copyright, Abstract, and so on. However
it might be desirable to fetch out just the citation tags as a series of Stones. In this case, you can declare Citation to be the top
level tag by passing the -tag argument to new(). Now calling get() will return each of the three Citation sections in turn. If no tag is
explicitly declared to be the top level tag, then Boulder::XML will take the first tag it sees in the document.
It is possible to stream XML files. You can either separate them into separate documents and use the automatic ARGV processing features of
the BoulderIO library, or separate the XML documents using a delimiter string similar to the delimiters used in MIME multipart documents.
By default, BoulderIO uses a delimiter of <!--Boulder::XML-->.
This is not a general XML parsing engine! Instead, it is a way to represent BoulderIO tag/value streams in XML format. The module uses
XML::Parser to parse the XML streams, and therefore any syntactic error in the stream can cause the XML parser to quit with an error.
Another thing to be aware of is that there are certain XML constructions that will not translate into BoulderIO format, specifically free
text that contains embedded tags. This is OK:
<Author>Jean Siao</Author>
but this is not:
<Author>The <Emphatic>extremely illustrious</Emphatic> Jean Siao</Author>
In BoulderIO format, tags can contain other tags or text, but cannot contain a mixture of tags and text.
CONSTRUCTORS
$stream = Boulder::XML->new(*IN,*OUT);
$stream = Boulder::XML->new(-in=>*IN, -out=>*OUT, -tag=>$tag, -delim=>$delim, -strip=>$strip)
new() creates a new Boulder::XML stream that can be read from or written to. All arguments are optional.
-in Filehandle to read from.
If a file name is provided, will open the file.
Defaults to the magic <> filehandle.
-out Filehandle to write to.
If a file name is provided, will open the file for writing.
Defaults to STDOUT
-tag The top-level XML tag to consider as the Stone record. Defaults
to the first tag seen when reading from an XML file, or to
E<lt>StoneE<gt> when writing to an output stream without
previously having read.
-delim Delimiter to use for delimiting multiple Stone objects in an
XML stream.
-strip If true, automatically strips leading and trailing whitespace
from text contained within tags.
$fh = Boulder::XML->newFh(*IN,*OUT);
$fh = Boulder::XML->newFh(-in=>*IN, -out=>*OUT, -tag=>$tag, -delim=>$delim, -strip=>$strip)
The newFh() constructor creates a tied filehandle that can read and write Boulder::XML streams. Invoking <> on the filehandle will
perform a get(), returning a Stone object. Calling print() on the filehandle will perform a put(), writing a Stone object to output in
XML format.
METHODS
$stone = $stream->get()
$stream->put($stone)
$done = $stream->done
All these methods have the same semantics as the similar methods in Boulder::Stream, except that pass-through behavior doesn't apply.
AUTHOR
Lincoln D. Stein <lstein@cshl.org>, 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::Stream, Stone
perl v5.10.1 2011-03-05 Boulder::XML(3pm)