better error handling for tests

parklab · Mar 7, 2018 · 1079908 · 1079908
1 parent d45a4fd
commit 1079908
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Showing 2 changed files with 16 additions and 14 deletions.
diff --git a/patterngenerator/makesnvpattern.pl b/patterngenerator/makesnvpattern.pl
@@ -1,22 +1,26 @@
 #!/usr/bin/perl
 ## the script assumes bowtie path is included.
 
+sub system2{
+  system(@_)==0 || die "$?";
+}
+
 if(@ARGV<5){ print "usage: $0 bedfile genomefasta genome(bowtie)index outdir outprefix\n"; exit;}
 my ($bedfile,$genomefasta,$genomeindex,$outdir,$outprefix)=@ARGV;
 if(!-d $outdir){ system("mkdir -p $outdir"); }
 my ($scriptdir)=$0=~/(.+\/)[^\/]+$/; 
-system("${scriptdir}snvbed2patternfile.3.pl $bedfile $genomefasta > $outdir/$outprefix.txt");
-system("${scriptdir}patternfile2fasta.pl $outdir/$outprefix.txt > $outdir/$outprefix.fasta");
-system("bowtie -f -p 4 -v 0 -a $genomeindex $outdir/$outprefix.fasta > $outdir/$outprefix.bowtieout");
-system("${scriptdir}parse.pattern.bowtie.pl $outdir/$outprefix.bowtieout > $outdir/$outprefix.ntm");
-system("${scriptdir}filter_patters_based_on_ntm.pl $outdir/$outprefix.txt $outdir/$outprefix.ntm > $outdir/$outprefix.uniq.txt");
-system("${scriptdir}patternconverter $outdir/$outprefix.uniq.txt $outdir/$outprefix.pt");
+system2("${scriptdir}snvbed2patternfile.3.pl $bedfile $genomefasta > $outdir/$outprefix.txt");
+system2("${scriptdir}patternfile2fasta.pl $outdir/$outprefix.txt > $outdir/$outprefix.fasta");
+system2("bowtie -f -p 4 -v 0 -a $genomeindex $outdir/$outprefix.fasta > $outdir/$outprefix.bowtieout");
+system2("${scriptdir}parse.pattern.bowtie.pl $outdir/$outprefix.bowtieout > $outdir/$outprefix.ntm");
+system2("${scriptdir}filter_patters_based_on_ntm.pl $outdir/$outprefix.txt $outdir/$outprefix.ntm > $outdir/$outprefix.uniq.txt");
+system2("${scriptdir}patternconverter $outdir/$outprefix.uniq.txt $outdir/$outprefix.pt");
 
 # test
 print("Checking pattern file...\n");
-system("${scriptdir}patterntestreader $outdir/$outprefix.pt $outdir/$outprefix.pt-txt");
-system("sort $outdir/$outprefix.pt-txt > $outdir/$outprefix.pt-txt.sorted");
-system("sort $outdir/$outprefix.uniq.txt > $outdir/$outprefix.uniq.txt.sorted");
+system2("${scriptdir}patterntestreader $outdir/$outprefix.pt $outdir/$outprefix.pt-txt");
+system2("sort $outdir/$outprefix.pt-txt > $outdir/$outprefix.pt-txt.sorted");
+system2("sort $outdir/$outprefix.uniq.txt > $outdir/$outprefix.uniq.txt.sorted");
 $diff=`diff $outdir/$outprefix.pt-txt.sorted $outdir/$outprefix.uniq.txt.sorted`;
 if($diff!~/\S/){
   print("pattern file looks good!\n");

diff --git a/tests/test.sh b/tests/test.sh
@@ -1,13 +1,11 @@
 #!/bin/bash
-set -e
 
 # patterngenerator test
-./patterngenerator/makesnvpattern.pl tests/SNP_GRCh37_hg19_woChr_21part.bed tests/GRCh37_21part.multi.fa tests/GRCh37_21part tests out
+./patterngenerator/makesnvpattern.pl tests/SNP_GRCh37_hg19_woChr_21part.bed tests/GRCh37_21part.multi.fa tests/GRCh37_21part tests out || exit $?
 
 # ngscheckmate_fastq test for the pattern file
-./ngscheckmate_fastq -1 tests/test_21part.fastq tests/out.pt
+./ngscheckmate_fastq -1 tests/test_21part.fastq tests/out.pt || exit $?
 
 # remove test pattern files
-rm tests/out*
+rm -rf tests/out*
 
-set +e