Update to v1.0.1

README.rst

@@ -32,6 +32,13 @@ Workflow
 
 .. image:: https://github.com/shao-lab/MAmotif/blob/master/docs/source/image/MAmotif_workflow.png
 
+Citation
+--------
+
+`Sun H, Wang J, Gong Z, Yao J, Wang Y, Xu J, Yuan GC, Zhang Y, Shao Z. Quantitative integration of epigenomic variation
+and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator
+at gene promoters. Cell discovery. 2018 Jul 10;4(1):38. <https://www.nature.com/articles/s41421-018-0045-y>`__
+
 Documentation
 -------------
 

conda-recipe/meta.yaml

@@ -1,11 +1,10 @@
 package:
   name: mamotif
-  version: 1.0
+  version: 1.0.1
 
 source:
-  fn: MAmotif-1.0.tar.gz
-  url: https://pypi.python.org/packages/e2/05/3672ba721cbe8eddab2e846feca9b154ff656591b8f75108f6751741a6e2/MAmotif-1.0.tar.gz
-  md5: 634caf4a377af1da12bffb635b1243b6
+  url: https://files.pythonhosted.org/packages/66/9b/af0baf9a9e15c4989c5b7033a4fcf5df63daa1e0f9418464cd33dddd9e72/MAmotif-1.0.1.tar.gz
+  sha256: 1aca1462e69b2d8e2f6bef9a6f37b9b50d70efd5f7f43068250a1070c32961e7
 
 build:
   number: 0

docs/source/conf.py

@@ -58,7 +58,7 @@
 # The short X.Y version.
 version = u'1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'1.0'
+release = u'1.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

mamotif/__init__.py

@@ -1 +1 @@
-__version__ = "1.1"
+__version__ = "1.0.1"

mamotif/cmdline.py

@@ -56,10 +56,6 @@ def argparser_config():
     group_advanced = parser.add_argument_group("Advanced arguments")
     group_advanced.add_argument("-n", dest="random_times", type=int, default=5,
                                 help="Times of permutation to test the enrichment of peak overlap between two samples.")
-    group_advanced.add_argument("-v", dest="overlap_dependent", action="store_true", default=False,
-                                help="With this option on, MAnorm will pick out biased/unbiased peaks in an "
-                                     "overlap-dependent manner. Biased peaks are only chosen from unique peaks, "
-                                     "and unbiased peaks are only chosen from common peaks.")
     group_advanced.add_argument("-p", dest="p_cutoff", type=float, default=0.01,
                                 help="P-value cutoff to define biased (sample 1/2-specific) peaks.")
     group_advanced.add_argument("--m_cutoff", dest="m_cutoff", type=float, default=1.0,
@@ -132,27 +128,24 @@ def main():
     else:
         distance_cutoff = peak_width / 2
     random_times = args.random_times
-    overlap_dependent = args.overlap_dependent
     p_cutoff = args.p_cutoff
     m_cutoff = args.m_cutoff
     output_all = args.output_all
     output_name = args.output_prefix
 
     manorm_workflow.main(peaks_file1=peaks_file1, peaks_file2=peaks_file2, reads_file1=reads_file1,
-                         reads_file2=reads_file2,
-                         shift_size1=shiftsize1, shift_size2=shiftsize2, peak_width=peak_width,
-                         distance_cutoff=distance_cutoff,
-                         random_times=random_times, overlap_dependent=overlap_dependent, m_cutoff=m_cutoff,
-                         p_cutoff=p_cutoff,
-                         output_all=output_all, output_name=output_name)
+                         reads_file2=reads_file2, shift_size1=shiftsize1, shift_size2=shiftsize2,
+                         peak_width=peak_width, summit_dis_cutoff=distance_cutoff,
+                         n_random=random_times, m_cutoff=m_cutoff, p_cutoff=p_cutoff,
+                         full_output=output_all, name1=None, name2=None, output_name=output_name)
 
     logging.basicConfig(level=logging.INFO, format="%(levelname)-8s @%(asctime)s: %(message)s", stream=sys.stderr,
                         datefmt="%m/%d/%Y %H:%M", filemode="w")
     genome_dir = args.genome
-    gene_file = args.gene
+    gene_file = os.path.abspath(args.gene)
     motif_file = args.motif
     motif_filter_file = args.motif_list
-    peak_file = output_name + '/' + output_name + '_all_peaks_MAvalues.xls'
+    peak_file = output_name + '/' + output_name + '_all_MAvalues.xls'
     peak_format = 'manorm'
     peak_length = args.peak_length
     control_file = None

mamotif/cmdline_integrate.py

@@ -37,7 +37,7 @@ def main():
     parser = argparser_config()
     args = parser.parse_args()
     pk = args.pk
-    refgene = args.refgene
+    refgene = os.path.abspath(args.refgene)
     motif = args.motif
     negative = args.negative
     correction = args.correction

setup.py

@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 from mamotif import __version__
 
-INSTALL_REQUIRES = ['MAnorm>=1.0', 'motifscan>=1.1']
+INSTALL_REQUIRES = ['MAnorm>=1.1.4', 'motifscan>=1.1.2']
 
 CLASSIFIERS = ['Development Status :: 3 - Alpha',
                'Environment :: Console',