File/folder name changes.

ChangeLog

@@ -1,3 +1,18 @@
+2013-12-16  Tao Liu  <vladimir.liu@gmail.com>
+	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  <taoliu@jimmy.harvard.edu>
 	Version 1.4.2
 

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

bin/macs14 → 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
 # ------------------------------------

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

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

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
 # ------------------------------------

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

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()

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',