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#!/usr/bin/env perl -w
# phylofoot.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;
# DEFAULTS - presumes scripts are run from example/ directory
# in the TFBS distribution
# default values for optional parameters
my $CONSERVATION_PERCENT = 70;
my $MATRIX_THRESHOLD_PERCENT = 80;
my $SLIDING_WINDOW = 50;
# Get command line options - if you are curious how this
# works, check the Getopt::Long module documentation.
my ($database_dir, $alignment_file, $help);
my @matrix_IDs = ();
my $conservation = $CONSERVATION_PERCENT;
my $threshold = $MATRIX_THRESHOLD_PERCENT;
my $window = $SLIDING_WINDOW;
GetOptions('help' => \$help,
'alignment_file=s' => \$alignment_file,
'database=s' => \$database_dir,
'matrix-id:s' => \@matrix_IDs,
'conservation:f' => \$conservation,
'threshold-score:f' => \$threshold,
'window-size:i' => \$window
);
if($help) {
pod2usage(-exitstatus=>0, -verbose=>2);
}
elsif (!($alignment_file and $database_dir)) {
pod2usage(1);
}
# parse both the comma-separated lists and individually specified
# matrix IDs:
@matrix_IDs = split (",", join(',',@matrix_IDs));
# 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);
# slurp the matrices into a TFBS::MatrixSet;
my $matrixset;
unless (scalar @matrix_IDs) { # if none are selected, we already have the set:
$matrixset = $db->get_MatrixSet(-matrixtype=>"PWM"); # retrieves all matrices from the db
}
else { # otherwise we retrieve inly the requested ones
$matrixset = $db->get_MatrixSet(-IDs => \@matrix_IDs,
-matrixtype=>"PWM");
}
# do the phylogenetic footprinting search of the sites
my $sitepairset = $matrixset->search_aln(-file=>$alignment_file,
-cutoff=>"$conservation",
-threshold=>"$threshold\%",
-windowsize => $window);
# print it out in GFF format
print $sitepairset->GFF;
# ANd that's it. Instead of simply printing GFF, you can e.g.
# - iterate through individual detected binding site pairs and extract
# the information you need
# - attach individual sittes as Bio::SeqFeature subclass objects
# to bioperl's Bio::Seq objects
# - collect the hit sequences and produce derived pattern matrices
# using TFBS::Pa
# - you tell me...
# The rest is usage message if the user requests help
# or fails to provide required parameters
__END__
=head1 NAME
phylofoot.pl - Phylogenetic footprinting example script
=head1 SYNOPSIS
./phylofoot.pl -a <alignment_file> -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<-a or --alignment-file> <alignment file name>
REQUIRED: Name of the pairwise alignment file in Clustal
format.
A sample database directory examples/sample_alignment.aln
is available in TFBS distribution.
=item B<-m or --matrix-id> <list of matrix IDs>
OPTIONAL: ID of the matrix from the database to scan the
alignment with.You can specify multiple matrices using
multiple -m switches or a single comma-separated lists of
IDs (NO spaces - e.g. -m M00001,M00021,N01921 ). You can
use a script called examples/list_matrices.pl in TFBS distribution
to list information for all matrices in a matrix database
of the FlatFileDir type.
DEFAULT: If no matrix IDs are specified, all matrices in
the database are used for the search;
=item B<-w or --window-size> <integer value>
OPTIONAL: The width of sliding window for calculating
the conservation profile of the submitted pairwise alignment.
DEFAULT: If not specified, the default value is 50 (nucleotides).
=item B<-c or --conservation> <percent value>
OPTIONAL: Conservation cutoff (in percent) for a region of
multiple alignment to include detected conserved sites into output.
DEFAULT: If not specified, the default value is 70 (%).
=item B<-t or --threshold-score> <percent value>
OPTIONAL: Threshold score (in percent) for a matrix match to
a subsequence.
DEFAULT: If not specified, the default value is 80 (%).
=back
=head1 DESCRIPTION
This is an example script that scans conserved regions of a
pairwise DNA sequence alignment with a set of matrices form
a flat file databases and produces GFF output. Its source code is
meant to be studied by bioinformaticians who wish to learn how to
use TFBS modules.
=cut
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