Package Bio :: Package Wise
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Package Bio.Wise

Submodules

Function Summary
  align(cmdline, pair, kbyte, force_type, dry_run, quiet, debug)
Returns a filehandle
  all_pairs(singles)
Generate pairs list for all-against-all alignments
  main()
  _build_align_cmdline(cmdline, pair, output_filename, kbyte, force_type, quiet)
  _test(*args, **keywds)

Variable Summary
str __version__ = '$Revision: 1.14 $'

Function Details

align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False)

Returns a filehandle

all_pairs(singles)

Generate pairs list for all-against-all alignments
>>> all_pairs(range(4))
[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]

_build_align_cmdline(cmdline, pair, output_filename, kbyte=None, force_type=None, quiet=False)

>>> os.environ["WISE_KBYTE"]="300000"
>>> _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/output", kbyte=100000)
'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output'

>>> _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/output_aa")
'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa'

Variable Details

__version__

Type:
str
Value:
'$Revision: 1.14 $'                                                    

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