TAMO.MD.Meme | index /home/David_Gordon/docs/TAMO/MD/Meme.py |
MDscan.py -- Interface / Wrapper for MDscan program.
Download MEME separately from author's website (see TAMO/paths.py for instructions)
This program is executable from the command line, and it runs the MEME with a
set of default parameters. Type "$TAMO/MD/Meme.py" for options.
(There aren't too many options at this point. This module is most useful for reading
output from previous MEME runs.)
Copyright (2005) Whitehead Institute for Biomedical Research (except as noted below)
All Rights Reserved
Author: David Benjamin Gordon
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ACGT = ['A', 'C', 'G', 'T'] YEAST_BG = {'A': 0.31, 'C': 0.19, 'G': 0.19, 'T': 0.31} one2two = {'K': 'GT', 'M': 'AC', 'R': 'AG', 'S': 'CG', 'W': 'AT', 'Y': 'CT'} revcomp = {' ': 'N', 'A': 'T', 'B': 'N', 'C': 'G', 'D': 'N', 'G': 'C', 'H': 'N', 'K': 'M', 'M': 'K', 'N': 'N', ...} revcompTBL = '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\x1d\x1e\x1f !"#$%&\'()*+,-./...\xcf\xd0\xd1\xd2\xd3\xd4\xd5\xd6\xd7\xd8\xd9\xda\xdb\xdc\xdd\xde\xdf\xe0\xe1\xe2\xe3\xe4\xe5\xe6\xe7\xe8\xe9\xea\xeb\xec\xed\xee\xef\xf0\xf1\xf2\xf3\xf4\xf5\xf6\xf7\xf8\xf9\xfa\xfb\xfc\xfd\xfe\xff' revcomplement_memo = {'A': 'T'} two2one = {'AC': 'M', 'AG': 'R', 'AT': 'W', 'CG': 'S', 'CT': 'Y', 'GT': 'K'} |