Merge pull request #345 from deeptools/release2.2.1

Release 2.2.1

docs/content/News.rst

@@ -1,9 +1,18 @@
 News and Developments
 =====================
 
+
+Release 2.2.1
+-------------
+**7 February 2019**
+
+- Muting log output of matplotlib and cooler
+- Set version number of hicmatrix to 5, reason is version 5 depends on cooler version 0.7.11 and hicmatrix version 6 on 0.8.2. This cooler version has a significant performance drop for writing matrices.
+- Optional parameter for hicInfo to write the result to a file instead to the bash
+
 Release 2.2
 -----------
-**10 December 2018**
+**18 January 2019**
 
 This release contains:
 

docs/content/installation.rst

@@ -17,14 +17,15 @@ Requirements
 * pytables >= 3.4
 * pyBigWig >= 0.3
 * future >= 0.17
-* cooler >= 0.7.11
 * six >= 1.11
 * jinja2 >= 2.10
 * pandas >= 0.23
 * unidecode >= 1.0
-* hicmatrix >= 5
+* hicmatrix = 5
 * pygenometracks >= 2.1
 * psutil >= 5.4.8
+* hic2cool >= 0.4
+
 
 Command line installation using ``conda``
 -----------------------------------------

hicexplorer/__init__.py

@@ -1,5 +1,8 @@
 import logging
 logging.basicConfig(level=logging.INFO)
+logging.getLogger('matplotlib').setLevel(logging.WARNING)
+logging.getLogger('cooler').setLevel(logging.WARNING)
+
 import warnings
 import sys
 

hicexplorer/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '2.2'
+__version__ = '2.2.1'

hicexplorer/hicInfo.py

@@ -33,7 +33,9 @@ def parse_arguments(args=None):
                                 required=True)
 
     parserOpt = parser.add_argument_group('Optional arguments')
-
+    parserOpt.add_argument('--outFileName', '-o',
+                           help='File name to save information of the matrix instead of writing it to the bash.'
+                           )
     parserOpt.add_argument('--help', '-h', action='help', help='show this help message and exit')
 
     parserOpt.add_argument('--version', action='version',
@@ -58,14 +60,29 @@ def main():
 
         chromosomes = list(hic_ma.chrBinBoundaries)
 
-        print("File:\t{}".format(matrix))
-        print("Size:\t{:,}".format(size))
-        print("Sum:\t{:,}".format(sum_elements))
-        print("Bin_length:\t{}".format(bin_length))
-        print("Chromosomes:\t{}".format(", ".join(toString(chromosomes))))
-        print("Non-zero elements:\t{:,}".format(num_non_zero))
-        print("Minimum (non zero):\t{}".format(min_non_zero))
-        print("Maximum:\t{}".format(max_non_zero))
-        print("NaN bins:\t{}".format(num_nan_bins))
-        if check_cooler(matrix):
-            hic_ma.getInformationCoolerBinNames()
+        if args.outFileName:
+            with open(args.outFileName, 'w') as file:
+                file.write("# Matrix information file. Created with HiCExplorer's hicInfo version {}\n".format(__version__))
+                file.write("File:\t{}\n".format(matrix))
+                file.write("Size:\t{:,}\n".format(size))
+                file.write("Sum:\t{:,}\n".format(sum_elements))
+                file.write("Bin_length:\t{}\n".format(bin_length))
+                file.write("Chromosomes:\t{}\n".format(", ".join(toString(chromosomes))))
+                file.write("Non-zero elements:\t{:,}\n".format(num_non_zero))
+                file.write("Minimum (non zero):\t{}\n".format(min_non_zero))
+                file.write("Maximum:\t{}\n".format(max_non_zero))
+                file.write("NaN bins:\t{}\n".format(num_nan_bins))
+                if check_cooler(matrix):
+                    file.write('The following columns are available: {}'.format(hic_ma.getInformationCoolerBinNames()))
+        else:
+            print("File:\t{}".format(matrix))
+            print("Size:\t{:,}".format(size))
+            print("Sum:\t{:,}".format(sum_elements))
+            print("Bin_length:\t{}".format(bin_length))
+            print("Chromosomes:\t{}".format(", ".join(toString(chromosomes))))
+            print("Non-zero elements:\t{:,}".format(num_non_zero))
+            print("Minimum (non zero):\t{}".format(min_non_zero))
+            print("Maximum:\t{}".format(max_non_zero))
+            print("NaN bins:\t{}".format(num_nan_bins))
+            if check_cooler(matrix):
+                print('The following columns are available: {}'.format(hic_ma.getInformationCoolerBinNames()))

hicexplorer/utilities.py

@@ -490,6 +490,6 @@ def remove_non_ascii(pText):
 
 
 def check_cooler(pFileName):
-    if pFileName.endswith('.cool') or cooler.io.is_cooler(pFileName) or'.mcool' in pFileName:
+    if pFileName.endswith('.cool') or cooler.fileops.is_cooler(pFileName) or'.mcool' in pFileName:
         return True
     return False

requirements.txt

@@ -13,5 +13,6 @@ future >= 0.17.*
 unidecode >= 1.0.*
 hic2cool >= 0.4.*
 psutil >= 5.4.8
-hicmatrix >= 5
+hicmatrix >= 7
+cooler >= 0.8.2
 pygenometracks >= 2.1

setup.py

@@ -104,10 +104,10 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
                        "pyBigWig >= 0.3.*",
                        "six >= 1.11.*",
                        "future >= 0.17.*",
-                       "cooler >= 0.7.11*",
+                       "cooler >= 0.8.2*",
                        "jinja2 >= 2.10.*",
                        "unidecode >= 1.0.*",
-                       "hicmatrix >= 5",
+                       "hicmatrix >= 7",
                        "pygenometracks >= 2.1",
                        "psutil >= 5.4.8",
                        "hic2cool >= 0.4"