Merge pull request #259 from deeptools/fixenrichedContacts

Fix enriched contacts

hicexplorer/HiCMatrix.py

@@ -1269,6 +1269,9 @@ def save_lieberman(self, fileName):
                 fileh.close()
 
     def save_GInteractions(self, fileName):
+        """
+        Saves the matrix using bioconductor's GInteraction format. `bin_pos1 , bin_pos2, number of interactions`
+        """
         self.restoreMaskedBins()
         log.debug(self.matrix.shape)
         mat_coo = triu(self.matrix, k=0, format='csr').tocoo()

hicexplorer/hicFindEnrichedContacts.py

@@ -25,6 +25,9 @@ def parse_arguments(args=None):
 
     parserRequired = parser.add_argument_group('Required arguments')
 
+    parserRequired.add_argument('--matrix', '-m',
+                                help='Input matrix.',
+                                required=True)
     parserRequired.add_argument('--outFileName', '-o',
                                 help='File name to save the resulting matrix.',
                                 type=hicexplorer.parserCommon.writableFile,
@@ -50,7 +53,7 @@ def parse_arguments(args=None):
         action='store_true')
 
     parserOpt.add_argument(
-        '--depth',
+        '--maxDepth',
         help='Depth (in base pairs) up to which the computations will be carried out. A depth of 10.0000 bp '
              'means that any computations involving bins that are over 10kbp apart are not considered.',
         type=int,
@@ -812,8 +815,8 @@ def main(args=None):
         hic_ma.diagflat()
 
     if args.method == 'obs/exp':
-        hic_ma.convert_to_obs_exp_matrix(maxdepth=args.depth, perchr=args.perchr)
+        hic_ma.convert_to_obs_exp_matrix(maxdepth=args.maxDepth, perchr=args.perchr)
     else:
-        hic_ma.convert_to_zscore_matrix(maxdepth=args.depth, perchr=args.perchr)
+        hic_ma.convert_to_zscore_matrix(maxdepth=args.maxDepth, perchr=args.perchr)
 
     hic_ma.save(args.outFileName)

hicexplorer/hicFindTADs.py

@@ -1111,6 +1111,7 @@ def compute_spectra_matrix(self, perchr=True):
             pool = multiprocessing.Pool(self.num_processors)
             log.info("Using {} processors\n".format(self.num_processors))
             res = pool.map_async(func, TASKS).get(9999999)
+            pool.close()
         else:
             res = map(func, TASKS)