MeltDBWiki/ListAnnotations - Revision history

Admin: 4 revisions

2011-10-26T06:13:05Z

4 revisions

← Older revision	Revision as of 08:13, 26 October 2011
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imported>HeikoNeuweger at 10:37, 4 April 2008

2008-04-04T10:37:05Z

← Older revision		Revision as of 12:37, 4 April 2008
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	__NOTOC__		__NOTOC__
	~~[[ListAnnotations]]~~		=== List Peak Annotations ===

	* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.		* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.

imported>HeikoNeuweger at 10:36, 4 April 2008

2008-04-04T10:36:21Z

← Older revision		Revision as of 12:36, 4 April 2008
Line 4:		Line 4:
	* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.		* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.


	<pre><nowiki>		<pre><nowiki>
	#!/usr/bin/env perl		#!/usr/bin/env perl
Line 99:		Line 99:
	}		}

	</nowiki></pre>		</nowiki></pre>


	The output of the script consists of two tab separated columns, the first gives the ''Retention Time'' of the peak in seconds and the second columns contains the ''Description'' of the latest annotation.		* The output of the script consists of two tab separated columns, the first gives the ''Retention Time'' of the peak in seconds and the second columns contains the ''Description'' of the latest annotation.



	<pre><nowiki>		<pre><nowiki>
	Retention Time Annotation		Retention Time Annotation
Line 113:		Line 113:
	823.45302 Xcalibur annotation: Leucin(158)		823.45302 Xcalibur annotation: Leucin(158)
	....		....
	</nowiki></pre>		</nowiki></pre>

imported>HeikoNeuweger at 10:35, 4 April 2008

2008-04-04T10:35:43Z

← Older revision		Revision as of 12:35, 4 April 2008
Line 4:		Line 4:
	* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.		* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.


	<pre><nowiki>		<pre><nowiki>

	#!/usr/bin/env perl		#!/usr/bin/env perl



	use strict;		use strict;
Line 20:		Line 17:
	use Term::ReadKey;		use Term::ReadKey;
	use IO::Handle;		use IO::Handle;
	~~use Data::Dumper;~~



Line 34:		Line 29:
	"-c chromatogram name\n";		"-c chromatogram name\n";
	}		}


	# global variables		# global variables
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	}		}

			# initialize MeltDB master
	my $master = $app_frame->application_master();		my $master = $app_frame->application_master();

			# initialize MeltDB Chromatogram object
	my $chromatogram = $master->AC->Chromatogram->init_name($opt_c);		my $chromatogram = $master->AC->Chromatogram->init_name($opt_c);

	unless(ref $chromatogram){		unless(ref $chromatogram && $chromatogram->isa("MELT::DB::AC::Chromatogram")) {
	print "Error, could not $opt_c!\n";		print "Error, could not initialize $opt_c!\n";
	exit 1;		exit 1;
	}		}

			# generating the output

	print "Retention Time\tAnnotation\n";		print "Retention Time\tAnnotation\n";

	~~foreach my $peak (@{$master->Peak->fetchallby_chromatogram($chromatogram)}) {~~

			# fetch all peaks and sort them by retention time
			foreach my $peak (sort {$a->rt <=> $b->rt()} @{$master->Peak->fetchallby_chromatogram($chromatogram)}) {
	my $latest_anno = $peak->latest_annotation();		my $latest_anno = $peak->latest_annotation();
			# only peaks with annotations will be listed
	if (ref $latest_anno && $latest_anno->isa("MELT::DB::Annotation")) {		if (ref $latest_anno && $latest_anno->isa("MELT::DB::Annotation")) {
	print $peak->rt(), "\t", $latest_anno->description(), "\n";		print $peak->rt(), "\t", $latest_anno->description(), "\n";
	}		}

	}		}

	</nowiki></pre>		</nowiki></pre>

imported>HeikoNeuweger at 10:32, 4 April 2008

2008-04-04T10:32:31Z

New page

__NOTOC__
[[ListAnnotations]]

* This sample script will connect to your MeltDB Server and print all annotations associated to Peaks in your chromatogram.

<pre><nowiki>

#!/usr/bin/env perl

use strict;
use warnings;

use GPMS::Application_Frame::MELTDB;
use strict;
use Carp;
use Getopt::Std;
use Term::ReadKey;
use IO::Handle;
use Data::Dumper;

# this is necessary if the script is started via rsh(1)
# otherwise you won't see any output until the first <RETURN>
#
STDOUT->autoflush(1);

sub usage {
print "list latest peak annotation of a chromatogram in MeltDB.".
"-p project name\n".
"-c chromatogram name\n";
}

# global variables
our($opt_p, $opt_c);

getopts('p:c:');

# start sanity checks
if (!$opt_p) {
usage;
print "ERROR: Can't start script list_peak_annotations: No project name given!\n";
exit 1;
};

# start sanity checks
if (!$opt_c) {
usage;
print "ERROR: Can't start script list_peak_annotations: No chromatogram name given!\n";
exit 1;
};

my $usr = defined( $ENV{'LOGNAME'} ) ? $ENV{'LOGNAME'} : (getpwuid( $> ))[0];

print STDOUT "Enter your database password: ";
ReadMode('noecho');
my $password = ReadLine(0);
chomp $password;
print STDOUT "\n";
ReadMode('normal');

# initialize project
my $app_frame = GPMS::Application_Frame::MELTDB->new($usr,
$password);

unless(ref $app_frame){
print "Error, could not connect to database, wrong password?\n";
exit 1;
}

my $project_name = $opt_p;

unless($app_frame->project($project_name)){
print "Error, could not init project $project_name\n";
exit 1;
}

my $master = $app_frame->application_master();
my $chromatogram = $master->AC->Chromatogram->init_name($opt_c);

unless(ref $chromatogram){
print "Error, could not $opt_c!\n";
exit 1;
}

print "Retention Time\tAnnotation\n";

foreach my $peak (@{$master->Peak->fetchallby_chromatogram($chromatogram)}) {

my $latest_anno = $peak->latest_annotation();

if (ref $latest_anno && $latest_anno->isa("MELT::DB::Annotation")) {
print $peak->rt(), "\t", $latest_anno->description(), "\n";
}

}

</nowiki></pre>

The output of the script consists of two tab separated columns, the first gives the ''Retention Time'' of the peak in seconds and the second columns contains the ''Description'' of the latest annotation.

<pre><nowiki>
Retention Time Annotation
483.17202 Xcalibur annotation: Pyruvat(174)
556.99998 Xcalibur annotation: Alanin(116)
730.24998 Xcalibur annotation: Valin(144)
799.578 Xcalibur annotation: Urea(189)
823.45302 Xcalibur annotation: Leucin(158)
....
</nowiki></pre>