Merge pull request #884 from Clinical-Genomics/feature/pli_file

Feature/pli file

lib/MIP/File/Format/Pli.pm

@@ -0,0 +1,96 @@
+package MIP::File::Format::Pli;
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use strict;
+use utf8;
+use warnings;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+use Readonly;
+
+## MIPs lib/
+use MIP::Constants qw{ $COLON $NEWLINE $SPACE $TAB };
+
+BEGIN {
+    require Exporter;
+    use base qw{ Exporter };
+
+    # Set the version for version checking
+    our $VERSION = 1.00;
+
+    # Functions and variables which can be optionally exported
+    our @EXPORT_OK = qw{ load_pli_file };
+}
+
+sub load_pli_file {
+
+## Function : Load plI file values
+## Returns  :
+## Arguments: $infile_path    => Infile path
+##          : $log            => Log object
+##          : $pli_score_href => Pli scores hash
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $infile_path;
+    my $log;
+    my $pli_score_href;
+
+    my $tmpl = {
+        infile_path => {
+            defined     => 1,
+            required    => 1,
+            store       => \$infile_path,
+            strict_type => 1,
+        },
+        log => {
+            defined  => 1,
+            required => 1,
+            store    => \$log,
+        },
+        pli_score_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$pli_score_href,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my $FILEHANDLE = IO::Handle->new();
+
+    open $FILEHANDLE, q{<}, $infile_path
+      or $log->logdie( q{Cannot open } . $infile_path . $COLON . $OS_ERROR, $NEWLINE );
+
+  LINE:
+    while (<$FILEHANDLE>) {
+
+        chomp;
+
+        ## Unpack line
+        my $line = $_;
+
+        ## Get hgnc symbol and pli score
+        my ( $hgnc_symbol, $pli_score ) = split $TAB, $line;
+
+        ## Skip header
+        next LINE if ( $pli_score eq q{pLI} );
+
+        ## Set rounded pli score to hash
+        $pli_score_href->{$hgnc_symbol} = sprintf q{%.2f}, $pli_score;
+    }
+    close $FILEHANDLE;
+    return 1;
+}
+
+1;

t/data/references/gnomad_pli_per_gene_-_r2.1.1-.txt

@@ -0,0 +1,2 @@
+HGNC_SYMBOL	pLI
+ADK	0.91234

t/load_pli_file.t

@@ -0,0 +1,87 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir catfile };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2017 };
+use Readonly;
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Fixtures qw{ test_log test_standard_cli };
+
+my $VERBOSE = 1;
+our $VERSION = 1.00;
+
+$VERBOSE = test_standard_cli(
+    {
+        verbose => $VERBOSE,
+        version => $VERSION,
+    }
+);
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = (
+        q{MIP::File::Format::Pli} => [qw{ load_pli_file }],
+        q{MIP::Test::Fixtures}    => [qw{ test_log test_standard_cli }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::File::Format::Pli qw{ load_pli_file };
+
+diag(   q{Test load_pli_file from Pli.pm v}
+      . $MIP::File::Format::Pli::VERSION
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Constants
+Readonly my $ADK_PLI => 0.91;
+
+my $log = test_log( {} );
+
+## Given a pli file
+my $pli_values_file_path =
+  catfile( $Bin, qw{ data references gnomad_pli_per_gene_-_r2.1.1-.txt } );
+my %pli_score;
+
+my $is_ok = load_pli_file(
+    {
+        infile_path    => $pli_values_file_path,
+        log            => $log,
+        pli_score_href => \%pli_score,
+    }
+);
+
+my %expected_pli_score = ( ADK => $ADK_PLI );
+
+## Then load plI file should return true
+ok( $is_ok, q{Loaded plI file} );
+
+## Then pli_score hash should be loaded with hgnc_symbol and corresponding pli score
+is_deeply( \%pli_score, \%expected_pli_score, q{Loaded plI data into hash} );
+
+done_testing();

vcfparser.pl

@@ -28,6 +28,7 @@
 use MIP::Check::Modules qw{ check_perl_modules };
 use MIP::Constants qw{ %ANALYSIS $COLON $COMMA $NEWLINE $SPACE $TAB };
 use MIP::File::Format::Feature_file qw{ read_feature_file };
+use MIP::File::Format::Pli qw{ load_pli_file };
 use MIP::Log::MIP_log4perl qw{ initiate_logger };
 use MIP::Script::Utils qw{ help };
 use MIP::Vcfparser qw{ define_select_data_headers define_snpeff_annotations };
@@ -171,6 +172,7 @@ BEGIN
     load_pli_file(
         {
             infile_path    => $pli_values_file_path,
+            log            => $log,
             pli_score_href => \%pli_score,
         }
     );
@@ -380,63 +382,6 @@ sub define_consequence_severity {
     return %consequence_severity;
 }
 
-sub load_pli_file {
-
-## Function : Load plI file values
-## Returns  :
-## Arguments: $infile_path    => Infile path
-##          : $pli_score_href => Pli scores hash
-
-    my ($arg_href) = @_;
-
-    ## Flatten argument(s)
-    my $infile_path;
-    my $pli_score_href;
-
-    my $tmpl = {
-        infile_path => {
-            defined     => 1,
-            required    => 1,
-            store       => \$infile_path,
-            strict_type => 1,
-        },
-        pli_score_href => {
-            default     => {},
-            defined     => 1,
-            required    => 1,
-            store       => \$pli_score_href,
-            strict_type => 1,
-        },
-    };
-
-    check( $tmpl, $arg_href, 1 ) or die q{Could not parse arguments!};
-
-    my $FILEHANDLE = IO::Handle->new();
-
-    open $FILEHANDLE, q{<}, $infile_path
-      or $log->logdie( q{Cannot open } . $infile_path . $COLON . $!, $NEWLINE );
-
-  LINE:
-    while (<$FILEHANDLE>) {
-
-        chomp;
-
-        ## Unpack line
-        my $line = $_;
-
-        ## Get hgnc symbol and pli score
-        my ( $hgnc_symbol, $pli_score ) = split $TAB, $line;
-
-        ## Skip header
-        next if ( $pli_score eq q{pLI} );
-
-        ## Set rounded pli score to hash
-        $pli_score_href->{$hgnc_symbol} = sprintf( "%.2f", $pli_score );
-    }
-    close $FILEHANDLE;
-    return;
-}
-
 sub read_infile_vcf {
 
 ##read_infile_vcf