Merge 1284218 into da0f402

lib/MIP/Vcfparser.pm

@@ -27,7 +27,11 @@ BEGIN {
     our $VERSION = 1.00;
 
     # Functions and variables which can be optionally exported
-    our @EXPORT_OK = qw{ build_interval_tree define_select_data_headers };
+    our @EXPORT_OK = qw{
+      build_interval_tree
+      define_select_data_headers
+      define_snpeff_annotations
+    };
 }
 
 sub build_interval_tree {
@@ -146,4 +150,33 @@ q{##INFO=<ID=No_hgnc_symbol,Number=.,Type=String,Description="Clinically relevan
     return %select_data;
 }
 
+sub define_snpeff_annotations {
+
+## Function : Defines the snpeff annotations that can be parsed and modified from snpeff
+## Returns  : %snpeff_cmd
+## Arguments: None
+
+    my %snpeff_cmd;
+
+    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{File} = q{SnpSift dbnsfp};
+    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{vcf_key} =
+      q{dbNSFP_GERP___RS};
+    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{info} =
+q{##INFO=<ID=GERP++_RS_prediction_term,Number=A,Type=String,Description="GERP RS conservation prediction term">};
+    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{File} =
+      q{SnpSift dbnsfp};
+    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{vcf_key} =
+      q{dbNSFP_phastCons100way_vertebrate};
+    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{info} =
+q{##INFO=<ID=phastCons100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhastCons conservation prediction term">};
+    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{File} =
+      q{SnpSift dbnsfp};
+    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{vcf_key} =
+      q{dbNSFP_phyloP100way_vertebrate};
+    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{info} =
+q{##INFO=<ID=phyloP100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhyloP conservation prediction term">};
+
+    return %snpeff_cmd;
+}
+
 1;

t/define_select_data_headers.t

@@ -62,7 +62,8 @@ diag(   q{Test define_select_data_headers from Vcfparser.pm v}
 my %select_data = define_select_data_headers();
 
 my $hgnc_symbol_info_header =
-  q?##INFO=<ID=HGNC_symbol,Number=.,Type=String,Description="The HGNC gene symbol">?;
+  q{##INFO=<ID=HGNC_symbol,Number=.,Type=String,Description="The HGNC gene symbol">};
+
 ## Then keys should exist and header info should be set
 ok( keys %select_data, q{Returned hash keys} );
 

t/define_snpeff_annotations.t

@@ -0,0 +1,75 @@
+#!/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 };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2014 };
+use Readonly;
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Fixtures qw{ 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::Vcfparser}      => [qw{ define_snpeff_annotations }],
+        q{MIP::Test::Fixtures} => [qw{ test_standard_cli }],
+    );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Vcfparser qw{ define_snpeff_annotations };
+
+diag(   q{Test define_snpeff_annotations from Vcfparser.pm v}
+      . $MIP::Vcfparser::VERSION
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Given snpeff annotations
+my %snpeff_cmd = define_snpeff_annotations();
+
+my $phastcons100way_vertebrate_prediction_term_file = q{SnpSift dbnsfp};
+
+## Then keys should exist and annotation info should be set
+ok( keys %snpeff_cmd, q{Returned hash keys} );
+
+is(
+    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{File},
+    $phastcons100way_vertebrate_prediction_term_file,
+    q{Got file info for annotation key}
+);
+
+done_testing();

vcfparser.pl

@@ -30,7 +30,7 @@
 use MIP::File::Format::Feature_file qw{ read_feature_file };
 use MIP::Log::MIP_log4perl qw{ initiate_logger };
 use MIP::Script::Utils qw{ help };
-use MIP::Vcfparser qw{ define_select_data_headers };
+use MIP::Vcfparser qw{ define_select_data_headers define_snpeff_annotations };
 
 our $USAGE = build_usage( {} );
 
@@ -282,36 +282,6 @@ sub build_usage {
 END_USAGE
 }
 
-sub define_snpeff_annotations {
-
-## Function : Defines the snpeff annotations that can be parsed and modified
-## Returns  : %snpeff_cmd
-## Arguments: None
-
-    my %snpeff_cmd;
-
-    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{File} =
-      q?SnpSift dbnsfp?;
-    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{vcf_key} =
-      q?dbNSFP_phastCons100way_vertebrate?;
-    $snpeff_cmd{snpeff}{phastCons100way_vertebrate_prediction_term}{info} =
-q?##INFO=<ID=phastCons100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhastCons conservation prediction term">?;
-
-    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{File} =
-      q?SnpSift dbnsfp?;
-    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{vcf_key} =
-      q?dbNSFP_phyloP100way_vertebrate?;
-    $snpeff_cmd{snpeff}{phyloP100way_vertebrate_prediction_term}{info} =
-q?##INFO=<ID=phyloP100way_vertebrate_prediction_term,Number=A,Type=String,Description="PhyloP conservation prediction term">?;
-
-    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{File} = q{SnpSift dbnsfp};
-    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{vcf_key} =
-      q{dbNSFP_GERP___RS};
-    $snpeff_cmd{snpeff}{q{GERP++_RS_prediction_term}}{info} =
-q?##INFO=<ID=GERP++_RS_prediction_term,Number=A,Type=String,Description="GERP RS conservation prediction term">?;
-    return %snpeff_cmd;
-}
-
 sub define_consequence_severity {
 
 ## Function : Defines the precedence of consequences for SO-terms