Merged from master

CHANGES

@@ -1,2 +1,5 @@
+## 0.3.2 (2019-04-26)
+- Added --add_region_columns to TFBScan
+
 ## 0.3.1 (2019-04-10)
 - Split motif ids between name/motif_id/output_prefix

setup.py

@@ -1,27 +1,15 @@
 import os
 import sys
 import re
-from setuptools import setup, Extension
-from setuptools.command.build_ext import build_ext as _build_ext
+from setuptools import setup, Extension, dist
 
-included_dirs = []
+#Test if numpy is installed
 try:
 	import numpy as np
-	included_dirs.append(np.get_include())
 except:
-	pass
-
-"""
-#Test if numpy is installed
-class build_ext(_build_ext):
-    def finalize_options(self):
-        _build_ext.finalize_options(self)
-        # Prevent numpy from thinking it is still in its setup process:
-        __builtins__.__NUMPY_SETUP__ = False
-        import numpy as np
-       	self.include_dirs.append(np.get_include())
-       	included_dirs.append(np.get_include())
-"""
+	#Else, fetch numpy if needed
+	dist.Distribution().fetch_build_eggs(['numpy'])
+	import numpy as np
 
 #Add cython modules depending on the availability of cython
 cmdclass = {}
@@ -33,15 +21,16 @@ def finalize_options(self):
 else:
 	use_cython = True
 
+#To compile or not to compile
 if use_cython:
-	ext_modules = [Extension("tobias.utils.ngs", ["tobias/utils/ngs.pyx"], include_dirs=included_dirs), #,sinclude[np.get_include()]),
-					Extension("tobias.utils.sequences", ["tobias/utils/sequences.pyx"], include_dirs=included_dirs), #include_dirs=[np.get_include()]),
-					Extension("tobias.utils.signals", ["tobias/utils/signals.pyx"], include_dirs=included_dirs)] #, include_dirs=[np.get_include()])]
+	ext_modules = [Extension("tobias.utils.ngs", ["tobias/utils/ngs.pyx"], include_dirs=[np.get_include()]),
+				Extension("tobias.utils.sequences", ["tobias/utils/sequences.pyx"], include_dirs=[np.get_include()]),
+				Extension("tobias.utils.signals", ["tobias/utils/signals.pyx"], include_dirs=[np.get_include()])]
 
 else:
-	ext_modules = [Extension("tobias.utils.ngs", ["tobias/utils/ngs.c"], include_dirs=included_dirs), #, include_dirs=[np.get_include()]),
-					Extension("tobias.utils.sequences", ["tobias/utils/sequences.c"], include_dirs=included_dirs), #, include_dirs=[np.get_include()]),
-					Extension("tobias.utils.signals", ["tobias/utils/signals.c"], include_dirs=included_dirs)] #, include_dirs=[np.get_include()])]
+	ext_modules = [Extension("tobias.utils.ngs", ["tobias/utils/ngs.c"], include_dirs=[np.get_include()]),
+					Extension("tobias.utils.sequences", ["tobias/utils/sequences.c"], include_dirs=[np.get_include()]),
+					Extension("tobias.utils.signals", ["tobias/utils/signals.c"], include_dirs=[np.get_include()])] 
 
 #Path of setup file to establish version
 setupdir = os.path.abspath(os.path.dirname(__file__))
@@ -54,6 +43,7 @@ def find_version(init_file):
 	else:
 		raise RuntimeError("Unable to find version string.")
 
+#Readme from git
 def readme():
 	with open('README.md') as f:
 		return f.read()
@@ -73,8 +63,6 @@ def readme():
 		ext_modules=ext_modules,
 		cmdclass=cmdclass,
 		setup_requires=["numpy"],
-		include_dirs=included_dirs,
-		#dependency_links=['https://github.com/jhkorhonen/MOODS/releases/download/v1.9.3/MOODS-python-1.9.3.tar.gz#egg=MOODS-python-1.9.3'],	
 		install_requires=[
 			'numpy',
 			'scipy',
@@ -87,6 +75,7 @@ def readme():
 			'xlsxwriter',
 			'adjustText',
 			'pyBigWig',
+			'MOODS-python',
 		],
 		scripts = ["tobias/utils/filter_important_factors.py"],
 		classifiers=[
@@ -95,5 +84,5 @@ def readme():
 			'Topic :: Scientific/Engineering :: Bio-Informatics',
 			'Programming Language :: Python :: 3'
 		],
-		zip_safe=True,
+		zip_safe=True
 		)

tobias/TOBIAS.py

@@ -14,11 +14,14 @@
 try:
 	import MOODS
 except:
-	sys.exit("ERROR: Package MOODS is not installed and is needed by TOBIAS. You can install it using:\n" +
-			"$ wget https://github.com/jhkorhonen/MOODS/releases/download/v1.9.3/MOODS-python-1.9.3.tar.gz\n" +
-			"$ tar xzvf MOODS-python-1.9.3.tar.gz\n" + 
+	sys.exit("ERROR: Package MOODS is not installed and is needed by TOBIAS. You can install it via conds using:\n"
+			"$ conda install moods -c bioconda\n\n"
+			"Or directly from source:\n"
+			"$ wget https://github.com/jhkorhonen/MOODS/releases/download/v1.9.3/MOODS-python-1.9.3.tar.gz\n"
+			"$ tar xzvf MOODS-python-1.9.3.tar.gz\n"
 			"$ cd  MOODS-python-1.9.3\n"
-			"$ python setup.py install")
+			"$ python setup.py install"
+			)
 
 #Import general 
 import argparse

tobias/__init__.py

@@ -1 +1 @@
-__version__ = "0.3.1"
+__version__ = "0.3.2"

tobias/motifs/tfbscan.py

@@ -49,7 +49,8 @@ def add_tfbscan_arguments(parser):
 	optional_arguments.add_argument('--gc', metavar="", type=lambda x: restricted_float(x,0,1), help='Set the gc content for background regions (default: will be estimated from fasta)')
 	optional_arguments.add_argument('--pvalue', metavar="", type=lambda x: restricted_float(x,0,1), help='Set p-value for motif matches (default: 0.0001)', default=0.0001)
 	optional_arguments.add_argument('--keep-overlaps', action='store_true', help='Keep overlaps of same motifs (default: overlaps are resolved by keeping best-scoring site)')
-
+	optional_arguments.add_argument('--add-region-columns', action='store_true', help="Add extra information columns (from 4th column) from --regions to the output .bed-file(s) (default: off)")
+
 	RUN = parser.add_argument_group('Run arguments')
 	RUN.add_argument('--split', metavar="<int>", type=int, help="Split of multiprocessing jobs (default: 100)", default=100)
 	RUN.add_argument('--cores', metavar="", type=int, help='Number of cores to use (default: 1)', default=1)
@@ -72,8 +73,13 @@ def motif_scanning(regions, args, motifs_obj):
 	for region in regions:
 
 		seq = fasta_obj.fetch(region.chrom, region.start, region.end)
-		region_TFBS = motifs_obj.scan_sequence(seq, region)		#Scan sequence
+		region_TFBS = motifs_obj.scan_sequence(seq, region)		#Scan sequence, returns list of OneRegion TFBS
 
+		#Add region columns if chosen
+		if args.add_region_columns:
+			for TFBS in region_TFBS:
+				TFBS.extend(region[3:])
+
 		#Check format of region chromosome and convert sites if needed
 		m = re.match(r"(.+)\:([0-9]+)\-([0-9]+)\s+.+", region.chrom)
 		if m: