def check_main_from_file(cmd, fasta, expected, in_fa_file, capsys):
in_fa_file.write(fasta)
argv = ['prog', cmd, str(in_fa_file)]
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert (out == expected)
def check_main_from_stdin(cmd, fasta, expected, capsys):
mod.sys.stdin = io.StringIO(fasta)
argv = ['prog', cmd, '-']
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert (out == expected)
def check_main_from_stdin(cmd, fasta, expected, capsys):
mod.sys.stdin = cStringIO.StringIO(fasta)
argv = ['prog', cmd, '-']
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert(out == expected)
def check_main_from_file(cmd, fasta, expected, in_fa_file, capsys):
in_fa_file.write(fasta)
argv = ['prog', cmd, str(in_fa_file)]
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert(out == expected)
def check_main_from_stdin_with_whitelist(cmd, fasta, expected,
in_whitelist_file, capsys):
mod.sys.stdin = io.StringIO(fasta)
argv = ['prog', '--zmw-whitelist-fn', in_whitelist_file, cmd, '-']
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert (out == expected)
def check_main_from_file_with_whitelist(cmd, fasta, expected,
in_whitelist_file, in_fa_file, capsys):
in_fa_file.write(fasta)
argv = [
'prog', '--zmw-whitelist-fn', in_whitelist_file, cmd,
str(in_fa_file)
]
mod.main(argv)
out, err = capsys.readouterr()
if expected != out:
print(out)
assert (out == expected)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass