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Accidental modification of unitig-caller command
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johnlees committed Feb 1, 2022
1 parent 35aab50 commit a15d4a4
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion test/run_test.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,9 @@

sys.stderr.write("Testing Bifrost call\n")
subprocess.run("unitig-caller --call --refs refs.txt --out test_call --pyseer --rtab", shell=True, check=True)
sys.stderr.write("Testing rtab\n")
subprocess.run("python test-calls.py --method rtab --test test_call.rtab --expected bifrost_call.rtab", shell=True, check=True) # checks results match
sys.stderr.write("Testing pyseer\n")
subprocess.run("python test-calls.py --method pyseer --test test_call.pyseer --expected bifrost_call.pyseer", shell=True, check=True) # checks results match

sys.stderr.write("Testing Bifrost query\n")
Expand All @@ -18,7 +20,7 @@
subprocess.run("python test-calls.py --method pyseer --test test_query.pyseer --expected bifrost_query.pyseer --strict", shell=True, check=True) # checks results match

sys.stderr.write("Testing simple mode\n")
subprocess.run("unitig-caller --simple --refs refs.txt --unitigs test_unitigs_simple.fasta --out simple_calls --strict", shell=True, check=True) # checks if can be run
subprocess.run("unitig-caller --simple --refs refs.txt --unitigs test_unitigs_simple.fasta --out simple_calls", shell=True, check=True) # checks if can be run
subprocess.run("python test-calls.py --method pyseer --test simple_calls.pyseer --expected simple_results.pyseer --strict", shell=True, check=True) # checks results match

sys.stderr.write("Tests completed\n")

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