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Package Bio :: Package Wise |
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Submodules | |
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Function Summary | |
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Returns a filehandle | |
Generate pairs list for all-against-all alignments | |
main()
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_test(*args,
**keywds)
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Variable Summary | |
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str |
__version__ = '$Revision: 1.12 $'
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Function Details |
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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 |
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__version__
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