2.1.0 package. Revised testing scripts.

ChangeLog

@@ -1,5 +1,5 @@
 2014-06-16  Tao Liu  <[email protected]>
-	MACS version 2.0.10 20140616
+	MACS version 2.1.0 20140616 (tag:rc)
 
 	* callpeak module
 

DEBIAN/builddeb.sh

@@ -21,5 +21,5 @@ python2.7 setup.py install --prefix=debian/usr/ --install-layout=deb
 #for f in `ls debian/usr/bin/*.py`;do mv ${f} ${f/.py/};done
 for f in `find debian/usr/lib/ -name '*.pyc'`;do rm -f ${f};done
 fakeroot dpkg-deb --build debian
-mv debian.deb macs2_2.0.10.deb
-echo "finished!"
+mv debian.deb macs2_2.1.0.deb
+echo "finished!"

DEBIAN/changelog

@@ -1,6 +1,12 @@
+MACS (2.1.0)
+
+  * Version 2.1.0.
+
+  * Read the included ChangeLog for detail.
+
 MACS (2.0.10)
 
-  * Read the included ChangeLog for detail. 
+  * Read the included ChangeLog for detail.
 
   * Made deb for macs2.
 

DEBIAN/control

@@ -1,12 +1,12 @@
 Package: macs2
-Version: 2.0.10
+Version: 2.1.0
 Priority: optional
 Maintainer: Tao Liu <[email protected]>
-Depends: python2.7, python2.7-numpy (>=1.3) 
+Depends: python2.7, python2.7-numpy (>=1.6) 
 Architecture: all
 Suggests: bowtie, bwa, maq, peakanalyzer
 Section: science
-Homepage: http://liulab.dfci.harvard.edu/MACS/
+Homepage: http://github.com/taoliu/MACS/
 Tag: Science, Biology, Bioinformatics, ChIP-seq
 Description: Model-based Analysis for ChIP-Seq
  With the improvement of sequencing techniques, chromatin
@@ -26,5 +26,8 @@ Description: Model-based Analysis for ChIP-Seq
    * Predict ChIP fragment size from + and - strand peaks from raw data
    * Calculate local bias around ChIP peaks using a Poisson model.
    * Allow multiple reads at the exact same position.
-   * Generate combined score track using Poisson CDF upper tail pvalue.
+   * Generate combined score track using Poisson CDF upper tail p/q-values, fold-enrichment and more.
+   * Support narrow and broad factor calling.
+   * Support Paired-End libraries.
+   * Support comparison between two conditions.
  .

DEBIAN/docs

@@ -1,4 +1,4 @@
-README
+README.rst
 ChangeLog
-INSTALL
+INSTALL.rst
 COPYING

INSTALL.rst

@@ -1,7 +1,7 @@
 ======================
 INSTALL Guide For MACS
 ======================
-Time-stamp: <2012-04-28 12:54:45 Tao Liu>
+Time-stamp: <2014-06-17 12:57:57 Tao Liu>
 
 Please check the following instructions to complete your installation.
 
@@ -11,28 +11,54 @@ Prerequisites
 Python version must be equal to *2.7* to run MACS. I recommend
 using the version *2.7.2*.
 
-Numpy_ (>=1.3.0) are required to run MACS v2. 
-
-.. _Numpy: http://www.scipy.org/Download
+Numpy_ (>=1.6) are required to run MACS v2. 
 
 GCC is required to compile ``.c`` codes in MACS v2 package, and python
 header files are needed. If you are using Mac OSX, I recommend you
 install Xcode; if you are using Linux, you need to make sure
 ``python-dev`` is installed.
 
-Cython_ (>=0.14.1) is required *only if* you want to regenerate ``.c``
+Cython_ (>=0.18) is required *only if* you want to regenerate ``.c``
 files from ``.pyx`` files using ``setup_w_cython.py`` script.
 
+.. _Numpy: http://www.scipy.org/Download
 .. _Cython: http://cython.org/
 
+Easy installation through PyPI
+==============================
+
+The easiest way to install MACS2 is through PyPI system. Get pip_ if
+it's not available in your system. *Note* if you have already
+installed numpy and scipy system-wide, you can use ```virtualenv
+--system-site-packages``` to let your virtual Python environment have
+access to system-wide numpy and scipy libraries so that you don't need
+to install them again.  
+
+Then under command line, type ```pip install MACS2```. PyPI will
+install Numpy and Scipy automatically if they are absent.  
+
+To upgrade MACS2, type ```pip install -U MACS2```. It will check
+currently installed MACS2, compare the version with the one on PyPI
+repository, download and install newer version while necessary.
+
+Note, if you do not want pip to fix dependencies. For example, you
+already have a workable Scipy and Numpy, and when 'pip install -U
+MACS2', pip downloads newest Scipy and Numpy but unable to compile and
+install them. This will fail the whole installation. You can pass
+'--no-deps' option to pip and let it skip all dependencies. Type
+```pip install -U --no-deps MACS2```.
+
+.. _pip: http://www.pip-installer.org/en/latest/installing.html
+
+
 Install under Debian or Ubuntu Linux system
 ===========================================
 
-The most convenient way to install MACS is through Debian APT system,
-so that it can be perfectly integrated in the Python environment of
-your operation system. You can easily manage the package, and the
-uninstallation is much easier. Download the *deb* package from MACS
-download page, and type this in the commend line::
+You can install MACS2 through Debian APT system, so that it can be
+perfectly integrated in the Python environment of your operation
+system. You can easily manage the package, and the uninstallation is
+much easier. Download the *deb* package from MACS download page, and
+type this in the commend line::
 
  $ dpkg -i macs_2.0.10.deb
 

MACS2/Constants.py

@@ -1,4 +1,4 @@
-MACS_VERSION = "2.0.10.20140616"
+MACS_VERSION = "2.1.0.20140616"
 #MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"
 FILTERDUP_VERSION = "1.0.0 20140616"
 RANDSAMPLE_VERSION = "1.0.0 20120703"

setup.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2014-06-17 12:00:10 Tao Liu>
+# Time-stamp: <2014-06-17 15:08:15 Tao Liu>
 
 """Description
 
@@ -57,7 +57,7 @@ def main():
                    ]
 
     setup(name="MACS2",
-          version="2.0.10.20140616",
+          version="2.1.0.20140616",
           description="Model Based Analysis for ChIP-Seq data",
           author='Tao Liu',
           author_email='[email protected]',

setup_w_cython.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2014-06-17 11:59:57 Tao Liu>
+# Time-stamp: <2014-06-17 15:11:17 Tao Liu>
 
 """Description: 
 
@@ -84,7 +84,7 @@ def main():
                        ]
 
     setup(name="MACS2",
-          version="2.0.10.20140616",
+          version="2.1.0.20140616",
           description="Model Based Analysis for ChIP-Seq data",
           author='Tao Liu',
           author_email='[email protected]',

test/test.sh

@@ -1,71 +1,76 @@
-python test_callsummits.py
-macs2 callpeak -t random_test.bed -g 10000 -n random_test_CS --nomodel --extsize 150 --call-summits -B
-macs2 callpeak -t random_test.bed -g 10000 -n random_test --nomodel --extsize 150
-macs2 refinepeak -b random_test_CS_summits.bed -i random_test.bed -o random_test
-bdg2bw random_test_CS_treat_pileup.bdg hg19.len
-bedtools sort -i random_test.bed | bedtools bedtobam -i - -g hg19.len > random_test.bam
-samtools index random_test.bam
-
-
 # test all sub-commands
 
 CHIP=ChIP_200K.bed.gz
 CTRL=Control_200K.bed.gz
 
 # callpeak
+echo "callpeak"
 
-macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_narrow -B --outdir run_callpeak_narrow
-macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_broad -B --outdir run_callpeak_broad --broad
+macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_narrow -B --outdir run_callpeak_narrow --call-summits &> run_callpeak_narrow/run_callpeak_narrow.log
+macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_narrow2 -B --outdir run_callpeak_narrow --nomodel --extsize 100 &> run_callpeak_narrow/run_callpeak_narrow2.log
+macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_narrow3 -B --outdir run_callpeak_narrow --nomodel --extsize 100 --shift -50 &> run_callpeak_narrow/run_callpeak_narrow3.log
+macs2 callpeak -t $CHIP -c $CTRL -n run_callpeak_broad -B --outdir run_callpeak_broad --broad &> run_callpeak_broad/run_callpeak_broad.log
 
 # bdgcmp
+echo "bdgcmp"
 
-macs2 bdgcmp -t run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg -c run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg -m ppois FE --outdir run_bdgcmp_oprefix --o-prefix run_bdgcmp_oprefix
+macs2 bdgcmp -t run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg -c run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg -m ppois FE --outdir run_bdgcmp_oprefix --o-prefix run_bdgcmp_oprefix &> run_bdgcmp_oprefix/run_bdgcmp_oprefix.log
 
-macs2 bdgcmp -t run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg -c run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg -m ppois FE --outdir run_bdgcmp_ofile -o run_bdgcmp_ofile_ppois.bdg run_bdgcmp_ofile_FE.bdg
+macs2 bdgcmp -t run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg -c run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg -m ppois FE --outdir run_bdgcmp_ofile -o run_bdgcmp_ofile_ppois.bdg run_bdgcmp_ofile_FE.bdg &> run_bdgcmp_ofile/run_bdgcmp_ofile.log
 
 # bdgpeakcall
+echo "bdgpeakcall"
 
-macs2 bdgpeakcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 2 --outdir run_bdgpeakcall --o-prefix run_bdgpeakcall_w_prefix
+macs2 bdgpeakcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 2 --outdir run_bdgpeakcall --o-prefix run_bdgpeakcall_w_prefix &> run_bdgpeakcall/run_bdgpeakcall_w_prefix.log
 
-macs2 bdgpeakcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 2 --outdir run_bdgpeakcall -o run_bdgpeakcall_w_ofile.narrowPeak
+macs2 bdgpeakcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 2 --outdir run_bdgpeakcall -o run_bdgpeakcall_w_ofile.narrowPeak &> run_bdgpeakcall/run_bdgpeakcall_w_ofile.log
 
 # bdgbroadcall
+echo "bdgbroadcall"
 
-macs2 bdgbroadcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 4 -C 2 --outdir run_bdgbroadcall --o-prefix run_bdgbroadcall_w_prefix
+macs2 bdgbroadcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 4 -C 2 --outdir run_bdgbroadcall --o-prefix run_bdgbroadcall_w_prefix &> run_bdgbroadcall/run_bdgbroadcall_w_prefix.log
 
-macs2 bdgbroadcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 4 -C 2 --outdir run_bdgbroadcall -o run_bdgbroadcall_w_ofile.gappedPeak
+macs2 bdgbroadcall -i run_bdgcmp_single/run_bdgcmp_single_myFE.bdg -c 4 -C 2 --outdir run_bdgbroadcall -o run_bdgbroadcall_w_ofile.gappedPeak &> run_bdgbroadcall/run_bdgbroadcall_w_ofile.log
 
 # diffpeak
 
 #NA
 
 # bdgdiff
+echo "bdgdiff"
 
-macs2 callpeak -c $CHIP -t $CTRL -n run_callpeak_narrow_revert -B --outdir run_callpeak_narrow_revert
+macs2 callpeak -c $CHIP -t $CTRL -n run_callpeak_narrow_revert -B --outdir run_callpeak_narrow_revert &> run_callpeak_narrow_revert/run_callpeak_narrow_revert.log
 
-macs2 bdgdiff --t1 run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg --c1 run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg --t2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg --o-prefix run_bdgdiff_prefix --outdir run_bdgdiff
+macs2 bdgdiff --t1 run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg --c1 run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg --t2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg --o-prefix run_bdgdiff_prefix --outdir run_bdgdiff &> run_bdgdiff/run_bdgdiff_w_prefix.log
 
-macs2 bdgdiff --t1 run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg --c1 run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg --t2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg -o cond1.bed cond2.bed common.bed --outdir run_bdgdiff
+macs2 bdgdiff --t1 run_callpeak_narrow/run_callpeak_narrow_treat_pileup.bdg --c1 run_callpeak_narrow/run_callpeak_narrow_control_lambda.bdg --t2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg -o cond1.bed cond2.bed common.bed --outdir run_bdgdiff &> run_bdgdiff/run_bdgdiff_w_o_file.log
 
 # filterdup
+echo "filterdup"
+
+macs2 filterdup -i $CHIP --outdir run_filterdup -o run_filterdup_result.bed --dry-run &> run_filterdup/run_filterdup_d.log
 
-macs2 filterdup -i $CHIP --outdir run_filterdup -o run_filterdup_result.bed
+macs2 filterdup -i $CHIP --outdir run_filterdup -o run_filterdup_result.bed &> run_filterdup/run_filterdup.log
 
 # predictd
+echo "predictd"
 
-macs2 predictd -i $CHIP --outdir run_predictd --rfile run_predictd.R
+macs2 predictd -i $CHIP --outdir run_predictd --rfile run_predictd.R &> run_predictd/run_predictd.log
 
 # pileup
+echo "pileup"
 
-macs2 pileup -i $CHIP --outdir run_pileup -o run_pileup.bdg
+macs2 pileup -i $CHIP --outdir run_pileup -o run_pileup.bdg &> run_pileup/run_pileup.log
 
 # randsample
+echo "randsample"
 
-macs2 randsample -t $CHIP -n 100000 --seed 31415926 --outdir run_randsample -o run_randsample.bed
+macs2 randsample -t $CHIP -n 100000 --seed 31415926 --outdir run_randsample -o run_randsample.bed &> run_randsample/run_randsample.log
 
 # refinepeak
+echo "refinepeak"
 
-macs2 refinepeak -b run_callpeak_narrow/run_callpeak_narrow_peaks.narrowPeak -i $CHIP --outdir run_refinepeak --o-prefix run_refinepeak_w_prefix
+macs2 refinepeak -b run_callpeak_narrow/run_callpeak_narrow_peaks.narrowPeak -i $CHIP --outdir run_refinepeak --o-prefix run_refinepeak_w_prefix &> run_refinepeak/run_refinepeak_w_prefix.log
 
-macs2 refinepeak -b run_callpeak_narrow/run_callpeak_narrow_peaks.narrowPeak -i $CHIP --outdir run_refinepeak -o run_refinepeak_w_ofile.bed
+macs2 refinepeak -b run_callpeak_narrow/run_callpeak_narrow_peaks.narrowPeak -i $CHIP --outdir run_refinepeak -o run_refinepeak_w_ofile.bed &> run_refinepeak/run_refinepeak_w_ofile.log