Merge pull request #26 from susannasiebert/perl_compile_test

Add compilation tests for all perl scripts
griffithlab · May 25, 2016 · 7fc6556 · 7fc6556
2 parents 17ed0b0 + 5a6c77a
commit 7fc6556
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Showing 4 changed files with 34 additions and 5 deletions.
diff --git a/t/GenerateFastaKey.t b/t/GenerateFastaKey.t
@@ -17,9 +17,12 @@ my $output_dir     = tempdir(CLEANUP => 1);
 my $sample_name             = 'Test';
 my $peptide_sequence_length = 21;
 
+my $generate_fasta_key_executable  = File::Spec->join($executable_dir, 'GenerateFastaKey.pl');
+my $compile_output = `$^X -c $generate_fasta_key_executable 2>&1`;
+like( $compile_output, qr/syntax OK$/, 'GenerateFastaKey script compiles' );
+
 my $generate_fasta_key_input_file  = File::Spec->join($test_data_dir, "${sample_name}_${peptide_sequence_length}.fa");
 my $generate_fasta_key_output_file = File::Spec->join($output_dir, "${sample_name}_${peptide_sequence_length}.key");
-my $generate_fasta_key_executable  = File::Spec->join($executable_dir, 'GenerateFastaKey.pl');
 my $generate_fasta_key_command = join(' ',
     "perl $generate_fasta_key_executable",
     "-i $generate_fasta_key_input_file",

diff --git a/t/GenerateVariantSequences.t b/t/GenerateVariantSequences.t
@@ -7,7 +7,7 @@ use Test::More;
 use File::Temp qw(tempdir);
 use Cwd qw(abs_path);
 use File::Basename qw(dirname);
-use File::Compare qw (compare);
+use File::Compare qw(compare);
 
 my $base_dir       = File::Spec->catdir(dirname(abs_path($0)), File::Spec->updir());
 my $executable_dir = File::Spec->catdir($base_dir, 'bin');
@@ -17,9 +17,12 @@ my $output_dir     = tempdir(CLEANUP => 1);
 my $sample_name             = 'Test';
 my $peptide_sequence_length = 21;
 
+my $generate_variant_sequences_executable  = File::Spec->join($executable_dir, 'GenerateVariantSequences.pl');
+my $compile_output = `$^X -c $generate_variant_sequences_executable 2>&1`;
+like( $compile_output, qr/syntax OK$/, 'GenerateVariantSequences script compiles' );
+
 my $generate_variant_sequences_input_file  = File::Spec->join($test_data_dir, 'annotated_variants.tsv');
 my $generate_variant_sequences_output_file = File::Spec->join($output_dir, "${sample_name}_${peptide_sequence_length}.fa");
-my $generate_variant_sequences_executable  = File::Spec->join($executable_dir, 'GenerateVariantSequences.pl');
 my $generate_variant_sequences_command = join(' ',
     "perl $generate_variant_sequences_executable",
     "-i $generate_variant_sequences_input_file",

diff --git a/t/ParseOutputNetmhc_and_BindingFilter.t b/t/ParseOutputNetmhc_and_BindingFilter.t
@@ -19,10 +19,13 @@ my $peptide_sequence_length = 21;
 my $epitope_length          = 9;
 my $allele                  = 'HLA-A29:02';
 
+my $parse_output_netmhc_executable  = File::Spec->join($executable_dir, 'ParseOutputNetmhc.pl');
+my $parse_output_netmhc_compile_output = `$^X -c $parse_output_netmhc_executable 2>&1`;
+like( $parse_output_netmhc_compile_output, qr/syntax OK$/, 'ParseOutputNetmhc script compiles' );
+
 my $parse_output_netmhc_input_file  = File::Spec->join($test_data_dir, "${sample_name}.${allele}.${epitope_length}.netmhc.xls");
 my $parse_output_netmhc_key_file    = File::Spec->join($test_data_dir, "${sample_name}_${peptide_sequence_length}.key");
 my $parse_output_netmhc_output_file = File::Spec->join($output_dir, "${sample_name}.${allele}.${epitope_length}.netmhc.parsed");
-my $parse_output_netmhc_executable  = File::Spec->join($executable_dir, 'ParseOutputNetmhc.pl');
 my $parse_output_netmhc_command = join(' ',
     "perl $parse_output_netmhc_executable",
     "-i $parse_output_netmhc_input_file",
@@ -35,13 +38,16 @@ ok(
     'ParseOutputNetmhc output as expected',
 );
 
+my $binding_filter_executable  = File::Spec->join($executable_dir, 'BindingFilter.pl');
+my $binding_filter_compile_output = `$^X -c $binding_filter_executable 2>&1`;
+like( $binding_filter_compile_output, qr/syntax OK$/, 'BindingFilter script compiles' );
+
 my $binding_filter_input_file  = File::Spec->join($test_data_dir, 'annotated_variants.tsv');
 my $binding_filter_output_fof  = File::Spec->join($output_dir, 'Test.fof');
 open(my $fh, '>', $binding_filter_output_fof);
 print $fh $parse_output_netmhc_output_file;
 close $fh;
 my $binding_filter_output_file = File::Spec->join($output_dir, "${sample_name}_filtered.xls");
-my $binding_filter_executable  = File::Spec->join($executable_dir, 'BindingFilter.pl');
 my $binding_filter_command = join(' ',
     "perl $binding_filter_executable",
     "-i $binding_filter_input_file",

diff --git a/t/pVAC-Seq.t b/t/pVAC-Seq.t
@@ -0,0 +1,17 @@
+#!/usr/bin/env genome-perl
+
+use strict;
+use warnings;
+
+use Test::More;
+use Cwd qw(abs_path);
+use File::Basename qw(dirname);
+use File::Spec;
+
+my $base_dir        = File::Spec->catdir(dirname(abs_path($0)), File::Spec->updir());
+my $pvac_seq_script = File::Spec->join($base_dir, 'pVAC-Seq.pl');
+
+my $compile_output = `$^X -c $pvac_seq_script 2>&1`;
+like( $compile_output, qr/syntax OK$/, 'pVAC-Seq script compiles' );
+
+done_testing;