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#!/usr/bin/env perl -w
# list_matrices.pl
# by Boris Lenhard
#
# See POD documentation for this script at the end of the file
#
use strict;
use Getopt::Long; # for parsing command line arguments
use Pod::Usage;
use TFBS::DB::FlatFileDir;
# Get command line options - if you are curious how this
# works, check the Getopt::Long module documentation.
my ($database_dir, $id_only, $verbose, $help);
GetOptions('help' => \$help,
'database=s' => \$database_dir,
'id-only' => \$id_only,
'verbose' => \$verbose
);
if($help) {
pod2usage(-exitstatus=>0, -verbose=>2);
}
elsif (!$database_dir) {
pod2usage(1);
}
# connect to FlatFileDir matrix database
# (there is a sample FlatFileDir matrix database directory
# examples/SAMPLE_FlatFileDir in the TFBS distribution package)
# Change this line if you want to use a different type of database
# (e.g. TFBS::DB::JASPAR2)
my $db = TFBS::DB::FlatFileDir->connect($database_dir);
# get all matrices (TFBS::Matrix::PWM objects) into a TFBS::MatrixSet object
my $matrixset = $db->get_MatrixSet(-matrixtype=>"PFM");
# print heading if normal output
unless ($id_only or $verbose) {
printf("\n %-10s%-15s%-20s%10s%10s\n",
'MatrixID', 'Name', 'Class','Length', 'Total IC');
}
# print line if normal or verbose output
unless($id_only) { print ("-"x70,"\n"); }
# Iterate through the set and display ID and name
# (aggregate classes in TFBS - TFBS::MatrixSet, TFBS::SiteSet,
# TFBS::SitePairSet) are equipped with iterators that all follow
# the same syntax:)
my $mx_iterator = $matrixset->Iterator(-sort_by=>'ID');
while (my $pfm = $mx_iterator->next()) { #for each matrix in the set
if ($verbose) {
print ("\n","-"x65);
print ("\nMatrix ID : ", $pfm->ID);
print ("\nTransctiption factor name : ", $pfm->name);
print ("\nStructural class : ", $pfm->class);
print ("\nTotal information content : ",
sprintf("%2.2f",$pfm->to_ICM->total_ic));
print ("\nMatrix:\n", $pfm->prettyprint);
print ("","-"x65,"\n\n");
}
elsif ($id_only) {
print ($pfm->ID, "\t", $pfm->name, "\n");
}
else {
printf(" %-10s%-15s%-20s%10s%10.2f\n",
$pfm->ID, $pfm->name, $pfm->class,
$pfm->length, $pfm->to_ICM->total_ic);
}
}
# print the line for normal and verbouse output
unless($id_only) {
print ("-"x70, "\nTotal ", $matrixset->size, " matrices.\n\n");
}
# The rest is usage message if the user requests help
# or fails to provide required parameters
__END__
=head1 NAME
list_matrices.pl - List info on matrix patterns stored in a flat file directory
=head1 SYNOPSIS
./list_matrices.pl -d <TFBS_matrix_dbase_dir> [other_options]
=head1 OPTIONS
=over 8
=item B<-d or --database> <directory name>
REQUIRED: Name of the FlatFileDir database directory to
use for retrieving matrices.
A sample database directory examples/SAMPLE_FlatFileDir
is available in TFBS distribution.
=item B<-i or --id-only>
OPTIONAL: Prints only a list of matrix IDs
=item B<-v or --verbose>
OPTIONAL: Prints full record (matrix and info). Overrides -i if set simultaneously.
=back
=head1 DESCRIPTION
This is an example script that displays information about matrix patterns stored
in a flat file directory-type database. Its source code is
meant to be studied by bioinformaticians who wish to learn how to
use TFBS modules.
=cut
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