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root/osprai/osprai/trunk/osprai_one.py
Revision: 65
Committed: Fri May 20 16:33:02 2011 UTC (8 years, 1 month ago) by clausted
File size: 2480 byte(s)
Log Message:
Added much testing to all modules using docstrings and doctest.  To help this, I also added two optional parameters to mclma(), verbose and maxiter.  For example, use "mclma(rois, verbose=False, maxiter=99)" to run the regression up to 99 iterations without echoing progress to the standard output.

Line User Rev File contents
1 clausted 21 """
2     osprai_one: Module to tie together the various osprai tools.
3     Christopher Lausted, Institute for Systems Biology,
4     Yuhang Wan, OSPRAI developers
5 clausted 49 Last modified on 110207 (yymmdd)
6 clausted 21
7     Examples:
8     from osprai_one import *
9     """
10 clausted 65 __version__ = "110519"
11 clausted 27 __all__ = ['BiosensorArray', 'RegOfInterest',
12 clausted 49 'readsprit', 'readclamp', 'readicmtxt', 'readbiosensor', 'readcsv',
13 clausted 27 'applygal', 'applykey', 'applymethod', 'writesprit',
14     'writeclamp', 'writebiosensor',
15     'dotgraph', 'linegraph', 'dualgraph', 'scatterplot',
16 clausted 36 'calibrate', 'bgset', 'bgsubt', 'copyinterval', 'zerotime', 'zerovalue',
17 clausted 27 'mclma', 'clma', 'lma',
18 clausted 65 'drift', 'drift_def_params', 'noise',
19     'simple1to1', 'simple1to1_def_params',
20 clausted 60 'simple1to1_mtl', 'simple1to1_mtl_def_params',
21     'simple1to1_series', 'simple1to1_series_def_params',
22 clausted 27 'deepcopy', 'exit', 'getcwd', 'date',
23     'arange', 'zeros',]
24 clausted 21
25    
26     ## Import from OSPRAI project libraries
27    
28     from ba_class import BiosensorArray
29 clausted 27 from ba_class import RegOfInterest
30 clausted 21
31     from io_module import readsprit
32     from io_module import readclamp
33     from io_module import readicmtxt
34     from io_module import readbiosensor
35 clausted 49 from io_module import readcsv
36 clausted 21 from io_module import applygal
37     from io_module import applykey
38     from io_module import applymethod
39     from io_module import writesprit
40     from io_module import writeclamp
41 clausted 27 from io_module import writebiosensor
42 clausted 21
43     from vu_module import dotgraph
44     from vu_module import linegraph
45     from vu_module import dualgraph
46     from vu_module import scatterplot
47    
48     from cal_module import calibrate
49     from cal_module import bgset
50     from cal_module import bgsubt
51 clausted 24 from cal_module import copyinterval
52 clausted 36 from cal_module import zerotime
53     from cal_module import zerovalue
54 clausted 21
55 clausted 27 from fit_module import mclma
56 clausted 21 from fit_module import clma
57     from fit_module import lma
58    
59 clausted 65 from mdl_module import noise
60 clausted 21 from mdl_module import drift
61 clausted 65 from mdl_module import drift_def_params
62 clausted 21 from mdl_module import simple1to1
63 clausted 60 from mdl_module import simple1to1_def_params
64 clausted 26 from mdl_module import simple1to1_mtl
65 clausted 60 from mdl_module import simple1to1_mtl_def_params
66     from mdl_module import simple1to1_series
67     from mdl_module import simple1to1_series_def_params
68 clausted 21
69    
70     ## Import from standard libraries.
71    
72     from copy import deepcopy
73     from sys import exit
74     from os import getcwd
75     from datetime import date
76     from numpy import arange
77     from numpy import zeros
78    
79 clausted 49 ################################# End of module #################################