First commit of MAPD analysis support in npg_tracking

lib/npg_tracking/data/mapd.pm

@@ -0,0 +1,91 @@
+package npg_tracking::data::mapd;
+
+use Moose;
+
+our $VERSION = '0';
+
+extends 'npg_tracking::data::reference';
+
+has 'bin_size' => (
+    isa => 'Num',
+    is => 'ro',
+    required => 0,
+);
+
+has 'read_length' => (
+    isa => 'Num',
+    is => 'ro',
+    required => 0,
+);
+
+with 'npg_tracking::data::mapd::find';
+
+__PACKAGE__->meta->make_immutable;
+
+no Moose;
+
+1;
+__END__
+
+=head1 NAME
+
+npg_tracking::data::mapd
+
+=head1 VERSION
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+A wrapper class for finding the location of MAPD files.
+
+=head1 SUBROUTINES/METHODS
+
+=head2 id_run
+
+=head2 position
+
+=head2 tag_index
+
+=head2 rpt_list
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+=head1 DEPENDENCIES
+
+=over
+
+=item Moose
+
+=back
+
+=head1 INCOMPATIBILITIES
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+Ruben Bautista E<lt>[email protected]<gt>
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2018 GRL
+
+This file is part of NPG.
+
+NPG is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+=cut

lib/npg_tracking/data/mapd/find.pm

@@ -0,0 +1,192 @@
+package npg_tracking::data::mapd::find;
+
+use Moose::Role;
+use Carp;
+use Readonly;
+use File::Spec;
+use npg_tracking::util::abs_path qw(abs_path);
+
+with qw/npg_tracking::data::reference::find/;
+
+requires qw/read_length bin_size/;
+
+our $VERSION = '0';
+
+Readonly::Scalar my $MAPPABILITY_FILE => 'Combined_%s_%s_%s_%dbases_mappable_bins_GCperc_INPUT.txt';
+Readonly::Scalar my $MAPPABILITY_BED_FILE => 'Combined_%s_%s_%s_%dbases_mappable_bins.bed';
+
+has 'mappablebins_path' => (
+    isa => 'Maybe[Str]',
+    is => 'ro',
+    lazy_build => 1,
+);
+
+has 'mappability_file' => (
+    isa => 'Maybe[Str]',
+    is => 'ro',
+    lazy_build => 1,
+);
+
+has 'mappability_bed_file' => (
+    isa => 'Maybe[Str]',
+    is => 'ro',
+    lazy_build => 1,
+);
+
+has 'chromosomes_path' => (
+    isa => 'Maybe[Str]',
+    is => 'ro',
+    lazy_build => 1,
+);
+
+has 'chromosomes_file' => (
+    isa => 'Maybe[Str]',
+    is => 'ro',
+    lazy_build => 1,
+);
+
+sub _build_mappablebins_path {
+    my $self = shift;
+    return $self->_find_path(q[MappableBINS]);
+}
+
+sub _build_chromosomes_path {
+    my $self = shift;
+    return $self->_find_path(q[chromosomes]);
+}
+
+sub _build_mappability_file {
+    my $self = shift;
+    return $self->_find_mappability_file(q[txt]);
+}
+
+sub _build_mappability_bed_file {
+    my $self = shift;
+    return $self->_find_mappability_file(q[bed]);
+}
+
+sub _build_chromosomes_file {
+    my $self = shift;
+    return $self->_find_file(q[chromosomes], q[txt]);
+}
+
+sub _find_path {
+    my ($self, $dir_name) = @_;
+    my $path;
+    my ($organism, $strain) = $self->parse_reference_genome($self->lims->reference_genome);
+    if ($organism && $strain) {
+        $path = abs_path($self->custom_analysis_repository . "/mapd/$organism/$strain/$dir_name");
+    }
+    return $path;
+}
+
+sub _find_file {
+    my ($self, $subfolder, $file_type) = @_;
+    my $path = $self->_find_path($subfolder);
+    my @files;
+    if ($path) {
+        @files = glob $path . q[/*.] . $file_type;
+    }
+    if (scalar @files > 1) {
+        croak qq[More than one $file_type file in $path];
+    }
+    if (scalar @files == 0) {
+        if ($subfolder && -d $subfolder) {
+            $self->messages->push(qq[Directory $subfolder exists, but no such *.$file_type file exist]);
+        }
+        return;
+    }
+    return $files[0];
+}
+
+sub _find_mappability_file {
+    my ($self, $file_type) = @_;
+    my @files;
+    my $mappablebins_path = $self->mappablebins_path;
+    if ($mappablebins_path) {
+        @files = glob $mappablebins_path . q[/*.] . $file_type;
+    }
+    if (scalar @files == 0) {
+        $self->messages->push(q[Directory ]. $mappablebins_path.
+                              q[ exists, but no such *.]. $file_type.
+                              q[ file(s) exist]);
+        return;
+    }
+    my $mappability_file;
+    if ($file_type eq q[bed]) {
+        $mappability_file = $MAPPABILITY_BED_FILE;
+    } elsif ($file_type eq q[txt]) {
+        $mappability_file = $MAPPABILITY_FILE;
+    }
+    my ($organism, $strain) = $self->parse_reference_genome($self->lims->reference_genome);
+    if ($organism && $strain) {
+        $mappability_file = sprintf $mappability_file,
+                            $organism,  $strain, $self->bin_size, $self->read_length;
+        $mappability_file = File::Spec->catfile($self->mappablebins_path, $mappability_file);
+        if (! -e $mappability_file) {
+            $self->messages->push(q[Mappability file ]. $mappability_file.
+                                  q[ not found in ]. $mappablebins_path);
+            return;
+        }
+    }
+    return $mappability_file;
+}
+
+1;
+__END__
+
+=head1 NAME
+
+npg_tracking::data::mapd::find
+
+=head1 SYNOPSIS
+
+  package MyPackage;
+  use Moose;
+  with qw{npg_tracking::data::mapd::find};
+
+
+=head1 DESCRIPTION
+
+A Moose role for finding the location of MAPD files.
+
+=head1 SUBROUTINES/METHODS
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+=head1 DEPENDENCIES
+
+=over
+
+=item Moose::Role
+
+=item Carp
+
+=back
+
+=head1 INCOMPATIBILITIES
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+Ruben Bautista
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2018 Genome Research Limited
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

lib/npg_tracking/data/reference/list.pm

@@ -51,6 +51,7 @@ Readonly::Scalar our $TAG_SETS_DIR       => q[tag_sets];
 Readonly::Scalar our $TAXON_IDS_DIR      => q[taxon_ids];
 Readonly::Scalar our $BIN_DIR            => q[bin];
 Readonly::Scalar our $ORG_NAME_DELIM     => q[_];
+Readonly::Scalar our $CUSTOM_ANALYSIS_DIR=> q[custom_analysis];
 
 Readonly::Scalar our $LAST             => -1;
 Readonly::Scalar our $SECOND_FROM_END  => -2;
@@ -597,6 +598,22 @@ sub ref_file_prefix {
     croak qq[Reference file with .fa or .fasta or .fna extension not found in $fasta_dir];
 }
 
+=head2 custom_analysis repository
+
+An absolute path to the custom_analysis repository.
+
+=cut
+has 'custom_analysis_repository' => (isa        => 'NPG_TRACKING_REFERENCE_REPOSITORY',
+                                     is         => 'ro',
+                                     required   => 0,
+                                     lazy_build => 1,
+);
+sub _build_custom_analysis_repository {
+    my $self = shift;
+    return catdir($self->repository, $CUSTOM_ANALYSIS_DIR);
+}
+
+
 no Moose::Role;
 
 1;

t/10-mapd-find.t

@@ -0,0 +1,70 @@
+use strict;
+use warnings;
+use Test::More tests => 2;
+use Test::Exception;
+use File::Basename;
+use File::Copy;
+use File::Find;
+use File::Path qw(make_path);
+use File::Spec::Functions qw(catfile catdir);
+use File::Spec qw(splitpath);
+use File::Temp qw(tempdir);
+
+my $tmp_repos = tempdir(CLEANUP => 1);
+local $ENV{NPG_WEBSERVICE_CACHE_DIR} = $tmp_repos;
+
+my $ref_dir = catdir($tmp_repos,'custom_analysis','mapd','Homo_sapiens','1000Genomes_hs37d5');
+make_path(catdir($ref_dir, 'MappableBINS'), catdir($ref_dir, 'chromosomes'));
+`touch $ref_dir/MappableBINS/Combined_Homo_sapiens_1000Genomes_hs37d5_100000_151bases_mappable_bins_GCperc_INPUT.txt`;
+`touch $ref_dir/MappableBINS/Combined_Homo_sapiens_1000Genomes_hs37d5_100000_151bases_mappable_bins.bed`;
+`touch $ref_dir/MappableBINS/Combined_Homo_sapiens_1000Genomes_hs37d5_500000_151bases_mappable_bins_GCperc_INPUT.txt`;
+`touch $ref_dir/MappableBINS/Combined_Homo_sapiens_1000Genomes_hs37d5_500000_151bases_mappable_bins.bed`;
+`touch $ref_dir/chromosomes/chr_list.txt`;
+
+my $central = 't/data/mapd/';
+
+use_ok('npg_tracking::data::mapd');
+
+local $ENV{'NPG_CACHED_SAMPLESHEET_FILE'} = catfile($central, 'metadata_cache', 'samplesheet_27128.csv');
+
+subtest 'find mapd files 1' => sub {
+    plan tests => 8;
+
+    my $test = npg_tracking::data::mapd->new(
+        id_run => 27128,
+        position => 1,
+        tag_index => 1,
+        repository => $tmp_repos,
+        read_length => 151,
+        bin_size => 100000,);
+
+    isa_ok($test, 'npg_tracking::data::mapd');
+
+    is($test->lims->reference_genome, 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)',
+        'reference genome ok');
+
+    like($test->custom_analysis_repository, qr/$tmp_repos\/custom_analysis/smx,
+        'custom analysis repository path is correct');
+
+    my ($organism, $strain) = $test->parse_reference_genome($test->lims->reference_genome);
+    my $mappablebins_path = catdir($tmp_repos, 'custom_analysis', 'mapd', $organism, $strain, 'MappableBINS');
+    my $chromosomes_path = catdir($tmp_repos, 'custom_analysis', 'mapd', $organism, $strain, 'chromosomes');
+
+    is($test->mappablebins_path, $mappablebins_path,
+        'mappablebins path is correct');
+
+    is($test->chromosomes_path, $chromosomes_path,
+        'chromosomes path is correct');
+
+    is(basename($test->mappability_file), 'Combined_Homo_sapiens_1000Genomes_hs37d5_100000_151bases_mappable_bins_GCperc_INPUT.txt',
+        'finds mappability file');
+
+    is(basename($test->mappability_bed_file), 'Combined_Homo_sapiens_1000Genomes_hs37d5_100000_151bases_mappable_bins.bed',
+        'finds mappability bed file');
+
+    is(basename($test->chromosomes_file), 'chr_list.txt',
+        'finds chromosomes list file');
+};
+
+
+1;