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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| #!/bin/bash | ||
|
|
||
| if [ "$1" == "path" ] | ||
| then | ||
| echo "Testing amrfinder command in your \$PATH" | ||
| which amrfinder | ||
| AMRFINDER=amrfinder | ||
| else | ||
| echo "Testing ./amrfinder" | ||
| AMRFINDER=./amrfinder | ||
| fi | ||
|
|
||
| if ! $AMRFINDER --plus -p test_prot.fa -g test_prot.gff -O Escherichia > test_prot.got \ | ||
| || ! diff -q test_prot.expected test_prot.got | ||
| then | ||
| echo "Test failed: " | ||
| echo " $AMRFINDER --plus -p test_prot.fa -g test_prot.gff -O Escherichia > test_prot.got" | ||
| echo " diff test_prot.expected test_prot.got " | ||
| exit 1 | ||
| fi | ||
|
|
||
| if ! $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got > test_dna.got \ | ||
| || ! diff -q test_dna.expected test_dna.got | ||
| then | ||
| echo "Test failed: " | ||
| echo " $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got > test_dna.got" | ||
| echo " diff test_dna.expected test_dna.got" | ||
| exit 1 | ||
| fi | ||
| if ! diff -q test_dna_mut_all.expected test_dna_mut_all.got | ||
| then | ||
| echo "Test failed: " | ||
| echo " $AMRFINDER --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got > test_dna.got" | ||
| echo " diff test_dna_mut_all.expected test_dna_mut_all.got" | ||
| exit 1 | ||
| fi | ||
|
|
||
| if ! $AMRFINDER --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia > test_both.got \ | ||
| || ! diff -q test_both.expected test_both.got | ||
| then | ||
| echo "Test failed: " | ||
| echo " $AMRFINDER --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia > test_both.got" | ||
| echo " diff test_both.expected test_both.got " | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "Success!" |