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2011-10-26T06:13:06Z

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imported>HeikoNeuweger at 11:52, 4 April 2008

2008-04-04T11:52:20Z

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__NOTOC__
=== List Chromatogram Alignment information ===

* List all computed alignment anchors for a reference 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;

# 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 "export_alignments - list aligned positions for a reference chromatogram.".
"-p project name -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 set latest annotation: No project 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);

foreach my $obs (@{$master->Observation->Chromatogram->Alignment()->fetchallby_reference_chromatogram($chromatogram)}) {
print $chromatogram->rawChromatogram()."\t".$obs->chromatogram->rawChromatogram()."\n";
foreach my $pair (@{$obs->index_pairs()}) {
print $pair->[0]."\t".$pair->[1]."\n";
}
}
</nowiki></pre>

* [[Media:MeltDBWiki$$ListAlignments$export_alignments.pl]]
* The output represents aligned scan indices. First column is the scan number in the reference chromatogram, the second is the scan index of the aligned peak in the second chromatogram.

<pre><nowiki>
glucoseA.cdf glucoseB.cdf
21 24
94 94
146 148
195 196
228 229
302 302
388 389
452 452
501 500
527 528
585 585
630 630
695 696
722 723
815 814
1060 1061
1077 1077
1091 1092
1143 1145
1191 1192
1270 1271
...
</nowiki></pre>

* [[Media:MeltDBWiki$$ListAlignments$result.txt]]

MeltDBWiki/ListAlignments - Revision history

Admin: 1 revision

imported>HeikoNeuweger at 11:52, 4 April 2008