def test_run():
try:
remfile = os.path.join(
tmpdir, "ref_prok_rep_genomes.05.tar.gz.md5")
create_mock_archives()
cmd = [
"getblastdb.py", "--database", "ref_prok_rep_genomes",
"--dbpath", "/blastdb/tmp", "--test", "--delete"]
os.chdir(tmpdir)
os.remove(remfile)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and not files.endswith(".md5")
):
os.remove(files)
G.run_subprocess(cmd)
file1 = os.path.join(
tmpdir, "md5_files", "ref_prok_rep_genomes.00.tar.gz.md5")
file2 = os.path.join(
tmpdir, "md5_files", "ref_prok_rep_genomes.05.tar.gz.md5")
assert os.path.isfile(file1) is True
assert os.path.isfile(file2) is True
check_all_files()
finally:
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def create_customblastdb(config, infile):
cmd = [
"makeblastdb", "-in", infile, "-parse_seqids", "-title",
"mockconservedDB", "-dbtype", "nucl", "-out", config.customdb
]
G.run_subprocess(cmd, printcmd=False, logcmd=False, printoption=False)
def create_customblastdb():
cmd = [
"makeblastdb", "-in", dbpath, "-parse_seqids", "-title",
"mockconservedDB", "-dbtype", "nucl", "-out", dbpath
]
G.run_subprocess(cmd, printcmd=False, logcmd=False, printoption=False)