From ef006d9e1fa296a2b02eff456b9f6b293ca2bd46 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Mon, 16 Dec 2013 15:11:57 -0500 Subject: [PATCH] File/folder name changes. --- ChangeLog | 15 +++++++++++++++ MANIFEST.in | 2 +- bin/{macs14 => macs} | 14 +++++++------- bin/wignorm | 10 +++++----- lib/Constants.py | 2 +- lib/OptValidator.py | 4 ++-- lib/OutputWriter.py | 4 ++-- lib/PeakDetect.py | 12 ++++++------ setup.py | 12 ++++++------ 9 files changed, 45 insertions(+), 30 deletions(-) rename bin/{macs14 => macs} (98%) diff --git a/ChangeLog b/ChangeLog index 9ce50e16..4c99b415 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,18 @@ +2013-12-16 Tao Liu + Version 1.4.3 + + * File/folder name changes + + Executable script has been renamed as 'macs' to be consistent with + 'macs2' in MACS2. + + macs14 -> macs + + MACS library path has been renamed as 'MACS1' to be consistent + with 'MACS2' in MACS2. + + MACS14 -> MACS1 + 2011-12-07 Tao Liu Version 1.4.2 diff --git a/MANIFEST.in b/MANIFEST.in index 49047c2d..be67e04d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,4 +1,4 @@ -include README COPYING ChangeLog INSTALL MANIFEST NEW_IN_MACS14 setup.py bin/macs14 bin/wignorm bin/elandmulti2bed bin/elandresult2bed bin/elandexport2bed bin/sam2bed +include README COPYING ChangeLog INSTALL MANIFEST NEW_IN_MACS14 setup.py bin/macs bin/wignorm bin/elandmulti2bed bin/elandresult2bed bin/elandexport2bed bin/sam2bed recursive-include lib *.py prune test prune web \ No newline at end of file diff --git a/bin/macs14 b/bin/macs similarity index 98% rename from bin/macs14 rename to bin/macs index 0cf6ee72..0d08254f 100644 --- a/bin/macs14 +++ b/bin/macs @@ -1,5 +1,5 @@ #!/usr/bin/env python -# Time-stamp: <2012-04-25 22:34:40 Tao Liu> +# Time-stamp: <2013-12-16 15:03:24 Tao Liu> """Description: MACS 1.4 main executable @@ -32,12 +32,12 @@ import gzip # ------------------------------------ # own python modules # ------------------------------------ -from MACS14.OptValidator import opt_validate -from MACS14.OutputWriter import * -from MACS14.Prob import binomial_cdf_inv -from MACS14.PeakModel import PeakModel,NotEnoughPairsException -from MACS14.PeakDetect import PeakDetect -from MACS14.Constants import * +from MACS1.OptValidator import opt_validate +from MACS1.OutputWriter import * +from MACS1.Prob import binomial_cdf_inv +from MACS1.PeakModel import PeakModel,NotEnoughPairsException +from MACS1.PeakDetect import PeakDetect +from MACS1.Constants import * # ------------------------------------ # Main function # ------------------------------------ diff --git a/bin/wignorm b/bin/wignorm index c7fa4cb4..f476fa85 100644 --- a/bin/wignorm +++ b/bin/wignorm @@ -1,5 +1,5 @@ #!/usr/bin/env python -# Time-stamp: <2011-03-15 12:32:34 Tao Liu> +# Time-stamp: <2013-12-16 15:04:02 Tao Liu> """Description: Call peaks from two wiggle file, one for treatment and one for control. @@ -27,10 +27,10 @@ from array import array from math import log as mathlog from math import asinh from optparse import OptionParser -from MACS14.IO import WiggleIO -from MACS14 import Prob -from MACS14.Prob import * -from MACS14.IO.FeatIO import * +from MACS1.IO import WiggleIO +from MACS1 import Prob +from MACS1.Prob import * +from MACS1.IO.FeatIO import * # ------------------------------------ # constants diff --git a/lib/Constants.py b/lib/Constants.py index 8c1f57b7..bea54c78 100644 --- a/lib/Constants.py +++ b/lib/Constants.py @@ -1,4 +1,4 @@ -MACS_VERSION = "1.4.2 20120305" +MACS_VERSION = "1.4.3 20131216" MAX_PAIRNUM = 1000 MAX_LAMBDA = 100000 FESTEP = 20 diff --git a/lib/OptValidator.py b/lib/OptValidator.py index 98daf82f..1a68e266 100644 --- a/lib/OptValidator.py +++ b/lib/OptValidator.py @@ -1,4 +1,4 @@ -# Time-stamp: <2011-12-15 12:39:02 Tao Liu> +# Time-stamp: <2013-12-16 15:01:52 Tao Liu> """Module Description @@ -23,7 +23,7 @@ import logging from subprocess import Popen, PIPE from math import log -from MACS14.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, ELANDExportParser, PairEndELANDMultiParser, SAMParser, BAMParser, BowtieParser, guess_parser +from MACS1.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, ELANDExportParser, PairEndELANDMultiParser, SAMParser, BAMParser, BowtieParser, guess_parser # ------------------------------------ # constants # ------------------------------------ diff --git a/lib/OutputWriter.py b/lib/OutputWriter.py index 149db4b5..f3b49d3d 100644 --- a/lib/OutputWriter.py +++ b/lib/OutputWriter.py @@ -1,4 +1,4 @@ -# Time-stamp: <2011-02-16 22:16:16 Tao Liu> +# Time-stamp: <2013-12-16 15:02:33 Tao Liu> """Module Description @@ -20,7 +20,7 @@ import os import sys from array import array -from MACS14.Constants import * +from MACS1.Constants import * # ------------------------------------ # constants diff --git a/lib/PeakDetect.py b/lib/PeakDetect.py index f1b3abd7..a03df24b 100644 --- a/lib/PeakDetect.py +++ b/lib/PeakDetect.py @@ -1,4 +1,4 @@ -# Time-stamp: <2011-06-21 10:59:08 Tao Liu> +# Time-stamp: <2013-12-16 15:02:45 Tao Liu> """Module Description @@ -18,16 +18,16 @@ from math import log as mathlog from array import array -from MACS14.OutputWriter import zwig_write,zbdg_write -from MACS14.IO.FeatIO import PeakIO,WigTrackI -from MACS14.Prob import poisson_cdf,poisson_cdf_inv -from MACS14.Constants import * +from MACS1.OutputWriter import zwig_write,zbdg_write +from MACS1.IO.FeatIO import PeakIO,WigTrackI +from MACS1.Prob import poisson_cdf,poisson_cdf_inv +from MACS1.Constants import * class PeakDetect: """Class to do the peak calling. e.g: - >>> from MACS14.PeakDetect import PeakDetect + >>> from MACS1.PeakDetect import PeakDetect >>> pd = PeakDetect(treat=treatdata, control=controldata, pvalue=pvalue_cutoff, d=100, scan_window=200, gsize=3000000000) >>> pd.call_peaks() >>> print pd.toxls() diff --git a/setup.py b/setup.py index a065f6d0..c96fcd14 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -# Time-stamp: <2011-12-07 17:24:20 Tao Liu> +# Time-stamp: <2013-12-16 14:23:02 Tao Liu> """Description @@ -40,12 +40,12 @@ def main(): author='Yong Zhang; Tao (Foo) Liu', author_email='zy@jimmy.harvard.edu; taoliu@jimmy.harvard.edu', url='http://liulab.dfci.harvard.edu/MACS/', - package_dir={'MACS14' : 'lib'}, - packages=['MACS14', 'MACS14.IO'], - scripts=['bin/macs14','bin/elandmulti2bed','bin/elandresult2bed','bin/elandexport2bed', + package_dir={'MACS1' : 'lib'}, + packages=['MACS1', 'MACS1.IO'], + scripts=['bin/macs','bin/elandmulti2bed','bin/elandresult2bed','bin/elandexport2bed', 'bin/sam2bed','bin/wignorm'], - console=['bin/macs14'], - app =['bin/macs14'], + console=['bin/macs'], + app =['bin/macs'], classifiers=[ 'Development Status :: 5 - productive', 'Environment :: Console',