_build_align_cmdline(cmdline,
pair,
output_filename,
kbyte=None,
force_type=None,
quiet=False)
| source code
|
Helper function to build a command line string (PRIVATE).
>>> os.environ["WISE_KBYTE"]="300000"
>>> if os.isatty(sys.stderr.fileno()):
... c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"),
... "/tmp/output", kbyte=100000)
... assert c == 'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output', c
... c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"),
... "/tmp/output_aa")
... assert c == 'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa', c
... else:
... c = _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"),
... "/tmp/output", kbyte=100000)
... assert c == 'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output', c
... c = _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"),
... "/tmp/output_aa")
... assert c == 'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa', c
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