Package Bio :: Package Wise
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Package Wise

source code

Submodules [hide private]

Functions [hide private]
 
_build_align_cmdline(cmdline, pair, output_filename, kbyte=None, force_type=None, quiet=False)
Helper function to build a command line string (PRIVATE).
source code
 
align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False)
Returns a filehandle
source code
 
all_pairs(singles)
Generate pairs list for all-against-all alignments
source code
 
main() source code
 
_test(*args, **keywds) source code
Variables [hide private]
  __package__ = 'Bio.Wise'
Function Details [hide private]

_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

all_pairs(singles)

source code 

Generate pairs list for all-against-all alignments

>>> all_pairs(range(4))
[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]