=head1 NAME
CLIPSeqTools::App::nucleotide_composition - Measure nucleotide composition along reads.
=head1 SYNOPSIS
clipseqtools nucleotide_composition [options/parameters]
=head1 DESCRIPTION
Measure nucleotide composition along reads.
=head1 OPTIONS
Input options for library.
--driver <Str> driver for database connection (eg. mysql,
SQLite).
--database <Str> database name or path to database file for file
based databases (eg. SQLite).
--table <Str> database table.
--host <Str> hostname for database connection.
--user <Str> username for database connection.
--password <Str> password for database connection.
--records_class <Str> type of records stored in database.
--filter <Filter> filter library. May be used multiple times.
Syntax: column_name="pattern"
e.g. keep reads with deletions AND not repeat
masked AND longer than 31
--filter deletion="def"
--filter rmsk="undef" .
--filter query_length=">31".
Operators: >, >=, <, <=, =, !=, def, undef
Output
--o_prefix <Str> output path prefix. Script will create and add
extension to path. [Default: ./]
Other options.
--plot call plotting script to create plots.
-v --verbose print progress lines and extra information.
-h -? --usage --help print help message
=cut
package CLIPSeqTools::App::nucleotide_composition;
$CLIPSeqTools::App::nucleotide_composition::VERSION = '0.1.7';
# Make it an app command
use MooseX::App::Command;
extends 'CLIPSeqTools::App';
#######################################################################
####################### Load External modules #####################
#######################################################################
use Modern::Perl;
use autodie;
use namespace::autoclean;
use List::Util qw(sum);
#######################################################################
########################## Consume Roles ##########################
#######################################################################
with
"CLIPSeqTools::Role::Option::Library" => {
-alias => { validate_args => '_validate_args_for_library' },
-excludes => 'validate_args',
},
"CLIPSeqTools::Role::Option::Plot" => {
-alias => { validate_args => '_validate_args_for_plot' },
-excludes => 'validate_args',
},
"CLIPSeqTools::Role::Option::OutputPrefix" => {
-alias => { validate_args => '_validate_args_for_output_prefix' },
-excludes => 'validate_args',
};
#######################################################################
######################## Interface Methods ########################
#######################################################################
sub validate_args {
my ($self) = @_;
$self->_validate_args_for_library;
$self->_validate_args_for_plot;
$self->_validate_args_for_output_prefix;
}
sub run {
my ($self) = @_;
warn "Starting analysis: nucleotide_composition\n";
warn "Validating arguments\n" if $self->verbose;
$self->validate_args();
my @nts = ('A', 'C', 'G', 'T', 'N');
warn "Creating reads collection\n" if $self->verbose;
my $reads_collection = $self->reads_collection;
$reads_collection->schema->storage->debug(1) if $self->verbose > 1;
warn "Measuring nucleotide composition\n" if $self->verbose;
my @nt_count;
$reads_collection->foreach_record_do( sub {
my ($rec) = @_;
my @nts = split(//, uc($rec->sequence));
for my $i (0..$#nts) {
$nt_count[$i]{$nts[$i]} += $rec->copy_number;
}
return 0;
});
warn "Creating output path\n" if $self->verbose;
$self->make_path_for_output_prefix();
warn "Printing results\n" if $self->verbose;
open (my $OUT1, '>', $self->o_prefix.'nucleotide_composition.tab');
say $OUT1 join("\t", 'position', map {$_.'_count'} (@nts, 'total'));
for (my $i=0; $i<@nt_count; $i++) {
my @counts = map {$nt_count[$i]{$_} || 0} @nts;
say $OUT1 join("\t", $i, @counts, sum(@counts));
}
close $OUT1;
if ($self->plot) {
warn "Creating plot\n" if $self->verbose;
CLIPSeqTools::PlotApp->initialize_command_class(
'CLIPSeqTools::PlotApp::nucleotide_composition',
file => $self->o_prefix.'nucleotide_composition.tab',
o_prefix => $self->o_prefix
)->run();
}
}
1;