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from subprocess import PIPE, Popen
import weblogo._transformseq
from . import data_stream
def _exec(args, outputtext, returncode=0, stdin=None): # type: ignore
if not stdin:
stdin = data_stream("cap.fa")
args = ["transformseq"] + args
p = Popen(args, stdin=stdin, stdout=PIPE, stderr=PIPE)
(out, err) = p.communicate()
if returncode == 0 and p.returncode > 0:
print(err)
assert returncode == p.returncode
if returncode == 0:
assert len(err) == 0
out = out.decode()
for item in outputtext:
assert item in out
stdin.close()
def test_malformed_options() -> None:
_exec(["--notarealoption"], [], 2)
_exec(["extrajunk"], [], 2)
_exec(["-I"], [], 2)
def test_help_option() -> None:
_exec(["-h"], ["options"])
_exec(["--help"], ["options"])
def test_version_option() -> None:
_exec(["--version"], weblogo._transformseq.__version__)
def test_clustal() -> None:
_exec(["-F", "clustal"], ["TCTTGTGATGTGGTTAACCAAT"])
def test_reverse() -> None:
_exec(["--reverse"], ["TAACCAATTGGTGTAGTGTTCT"])
def test_complement() -> None:
_exec(["--complement"], ["AGAACACTACACCAATTGGTTA"])
def test_seg() -> None:
_exec(["--seg"], ["XXXXXXXXXXXXXXXXXXXXXX"])
def test_subsample() -> None:
_exec(["--subsample", "0.4"], [])
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