added new module hicInfo that will print simple statistics of HiC mat…

…rices

bin/hicInfo

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+#-*- coding: utf-8 -*-
+
+from hicexplorer.hicInfo import main
+
+if __name__ == "__main__":
+    main()

hicexplorer/hicInfo.py

@@ -0,0 +1,45 @@
+import argparse
+from hicexplorer import HiCMatrix as hm
+from hicexplorer._version import __version__
+
+
+def parse_arguments(args=None):
+
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+                                     description=('Prints information about a matrix including size, '
+                                                  'number of elements, sum of elements, etc.'))
+
+    parser.add_argument('--matrices', '-m',
+                        help='matrices to add. Must have the same shape.',
+                        metavar='.h5 of .npz file format',
+                        nargs='+',
+                        required=True)
+
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s {}'.format(__version__))
+
+    return parser
+
+
+def main():
+
+    args = parse_arguments().parse_args()
+    for matrix in args.matrices:
+        print("File:\t{}".format(matrix))
+
+        hic_ma = hm.hiCMatrix(matrix)
+        size = hic_ma.matrix.shape[0]
+        num_non_zero = hic_ma.matrix.nnz
+        sum_elements = hic_ma.matrix.sum()/2
+        bin_length = hic_ma.getBinSize()
+        num_nan_bins = len(hic_ma.nan_bins)
+        chromosomes = hic_ma.chrBinBoundaries.keys()
+
+        print("Size:\t{:,}".format(size))
+        print("Sum:\t{:,}".format(sum_elements))
+        print("Bin_length:\t{}".format(bin_length))
+        print("Chromosomes:\t{}".format(", ".join(chromosomes)))
+        print("Non-zero elements:\t{:,}".format(num_non_zero))
+        print("NaN bins:\t{}".format(num_nan_bins))
+        print("")
+

setup.py

@@ -61,7 +61,7 @@ def get_version():
     scripts=['bin/findRestSite', 'bin/hicBuildMatrix', 'bin/hicCorrectMatrix',
              'bin/hicCorrelate', 'bin/hicFindEnrichedContacts', 'bin/hicFindTADs',
              'bin/hicMergeMatrixBins', 'bin/hicPlotMatrix', 'bin/hicPlotDistVsCounts',
-             'bin/hicPlotTADs', 'bin/hicSumMatrices', 'bin/hicExport'],
+             'bin/hicPlotTADs', 'bin/hicSumMatrices', 'bin/hicExport', 'bin/hicInfo'],
     include_package_data=True,
     package_data={'': ['config/hicexplorer.cfg']},
     url='http://hicexplorer.readthedocs.io',