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|
#!/bin/bash
testOK="true"
run_test()
{
# param : reads_file ref_file true_result prefix
MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
MindTheGap fill -bkpt output/$4_find.breakpoints -graph output/$4_find.h5 -out output/$4_fill 1> output/$4_fill.out 2> output/$4_fill.err
tmp1=output/$4_fill.insertions.fasta.tmp
tmp2=output/tmp2
grep -v "^>" output/$4_fill.insertions.fasta > $tmp1
grep -v "^>" $3 > $tmp2
diff $tmp1 $tmp2 1> /dev/null 2>&1
var=$?
if [ $var -eq 0 ]
then
eval $6="passed"
else
testOK="false" ; eval $6="FAILED"
fi
}
run_test_vcf()
{
# param : reads_file ref_file true_result prefix
MindTheGap find -in $1 -ref $2 -kmer-size 31 -out output/$4_find $5 1> output/$4_find.out 2> output/$4_find.err
sh compare_vcf.sh output/$4_find.othervariants.vcf $3 1> /dev/null 2>&1
var=$?
if [ $var -eq 0 ]
then
eval $6="passed"
else
testOK="false" ; eval $6="FAILED"
fi
}
mkdir -p output
output=""
output=$output"clean-insert : "
run_test reads/master.fasta references/deleted.fasta truths/insertion.fasta k-1 "-insert-only" retvalue
output=${output}${retvalue}
output=$output"\n13-inserts-ref10k : "
run_test reads/readref10K.fasta references/g10K_del.fasta truths/insert_ref10K.fasta 13i "-insert-only" retvalue
output=${output}${retvalue}
output=$output"\n1-SNP : "
run_test_vcf reads/master.fasta references/sSNP.fasta truths/truth_snp.vcf sSNP "-snp-only" retvalue
output=${output}${retvalue}
output=$output"\n3-SNP*2 : "
run_test_vcf reads/master.fasta references/multiSNP.fasta truths/multiSNP.vcf multiSNP "-snp-only" retvalue
output=${output}${retvalue}
output=$output"\nsnp-before-clean-insert : "
run_test reads/master.fasta references/deleted_before_SNP.fasta truths/insertion_before_SNP.fasta k-1_before_SNP "-no-deletion -homo-only" retvalue
output=${output}${retvalue}
#output=$output"\nsnp-begin-fuzzy : "
#run_test reads/beginfuzzySNP.fasta references/beginfuzzySNP.fasta truths/beginfuzzySNP.fasta beginfuzzySNP "-snp-only" retvalue
#output=${output}${retvalue}
output=$output"\nhetero-insert : "
run_test reads/deleted.fasta,reads/master.fasta references/deleted.fasta truths/insertion.fasta hete "-hete-only -max-rep 2" retvalue
output=${output}${retvalue}
output=$output"\ndeletion : "
run_test reads/deleted.fasta references/master.fasta truths/deletion.fasta deletion "-deletion-only" retvalue
output=${output}${retvalue}
output=$output"\nfuzzy-deletion : "
run_test reads/deletionfuzzy.fasta references/deletionfuzzy.fasta truths/deletionfuzzy.fasta deletionfuzzy "-deletion-only" retvalue
output=${output}${retvalue}
output=$output"\nn-in-solid-stretch : "
run_test reads/master.fasta references/n_in_stretch.fasta truths/n_in_stretch.fasta n_in_stretch "-insert-only" retvalue
output=${output}${retvalue}
output=$output"\nn-in-before-clean-insert : "
run_test reads/master.fasta references/n_before_gap.fasta truths/n_before_gap.fasta n_before_gap "-insert-only" retvalue
output=${output}${retvalue}
output=$output"\nn-after-clean-insert : "
run_test reads/master.fasta references/n_after_gap.fasta truths/n_after_gap.fasta n_after_gap "-insert-only" retvalue
output=${output}${retvalue}
echo -e $output | column -t
rm -rf output/
if [ $testOK == "false" ]; then
exit 1
fi
|
