Resolving merge conflicts and python 2 vs python 3 conflicts

docs/content/installation.rst

@@ -37,7 +37,7 @@ Command line installation using ``pip``
 
 Install HiCExplorer using the following command:
 ::
-
+--
 	$ pip install hicexplorer
 
 All python requirements should be automatically installed.

hicexplorer/HiCMatrix.py

@@ -283,7 +283,13 @@ def getDekkerBins(self, fileName):
         self.header = []
         try:
             for line in gzip.open(fileName, 'r').readlines():
-                if line.startswith(b"#"):
+                if type(line) is bytes:
+                    query = b"#"
+
+                if type(line) is str:
+                    query = "#"
+
+                if line.startswith(query):
                     self.header.append(line)
                     continue
                 i += 1

hicexplorer/hicBuildMatrix.py

@@ -1079,7 +1079,7 @@ def main(args=None):
         start_pos_coverage, end_pos_coverage)))
     start_pos_coverage = None
     end_pos_coverage = None
-    coverage = Array(c_uint, number_of_elements_coverage)
+    coverage = Array(c_uint, [0] * number_of_elements_coverage)
 
     # define global shared ctypes arrays for row, col and data
     args.threads = args.threads - 1

hicexplorer/hicFindTADs.py

@@ -1123,7 +1123,8 @@ def load_bedgraph_matrix(self, filename):
         end_list = []
         with open(filename, 'r') as fh:
             for line in fh:
-                if line.startswith(b"#"):
+                # if type(line)
+                if line.startswith("#"):
                     # recover the parameters used to generate the spectrum_matrix
                     parameters = json.loads(line[1:].strip())
                     continue

hicexplorer/hicPrepareQCreport.py

@@ -54,13 +54,13 @@ def save_html(filename, unmap_table, discard_table, distance_table, orientation_
     html = open(os.path.join(root, "qc_template.html"), "r")
     html_content = html.read()
     # the html code has a placeholder for the html table
-    html = html.replace("%%TABLE_UNMAP%%", unmap_table.style
+    html_content = html_content.replace("%%TABLE_UNMAP%%", unmap_table.style
                         .format(lambda x: '{:,}'.format(x) if x > 1 else '{:.2%}'.format(x)).render())
-    html = html.replace("%%TABLE_DISCARDED%%", discard_table.style
+    html_content = html_content.replace("%%TABLE_DISCARDED%%", discard_table.style
                         .format(lambda x: '{:,}'.format(x) if x > 1 else '{:.2%}'.format(x)).render())
-    html = html.replace("%%TABLE_DISTANCE%%", distance_table.style
+    html_content = html_content.replace("%%TABLE_DISTANCE%%", distance_table.style
                         .format(lambda x: '{:,}'.format(x) if x > 1 else '{:.2%}'.format(x)).render())
-    html = html.replace("%%TABLE_ORIENTATION%%", orientation_table.style
+    html_content = html_content.replace("%%TABLE_ORIENTATION%%", orientation_table.style
                         .format(lambda x: '{:,}'.format(x) if x > 1 else '{:.2%}'.format(x)).render())
 
     all_table = all_table[['Pairs considered', 'Pairs mappable, unique and high quality', 'Pairs used',
@@ -69,7 +69,7 @@ def save_html(filename, unmap_table, discard_table, distance_table, orientation_
                            'self circle', 'duplicated pairs', 'inter chromosomal', 'short range < 20kb',
                            'long range', 'inward pairs', 'outward pairs', 'left pairs', 'right pairs']]
 
-    html = html.replace("%%TABLE%%", all_table.style.render())
+    html_content = html_content.replace("%%TABLE%%", all_table.style.render())
     with open(filename, 'w') as fh:
         fh.write(html_content)
     html.close()

hicexplorer/test/test_buildMatrix.py

@@ -60,7 +60,7 @@ def test_build_matrix_rf():
                                                    qc_folder).split()
     hicBuildMatrix.main(args)
 
-    test = hm.hiCMatrix(ROOT + "small_test_rf_matrix_parallel.h5")
+    test = hm.hiCMatrix(ROOT + "small_test_rf_matrix.h5")
     new = hm.hiCMatrix(outfile.name)
     # print("MATRIX NAME RF:", outfile.name)
 

hicexplorer/trackPlot.py

@@ -746,11 +746,11 @@ def plot(self, ax, label_ax, chrom_region, start_region, end_region):
                 import pyBigWig
                 self.bw = pyBigWig.open(self.properties['file'])
 
-                print "error found while reading bigwig scores ({}).\nTrying again. Iter num: {}".format(e, num_tries)
+                print("error found while reading bigwig scores ({}).\nTrying again. Iter num: {}".format(e, num_tries))
                 pass
             else:
                 if num_tries > 1:
-                    print "After {} the scores could be computed".format(num_tries)
+                    print("After {} the scores could be computed".format(num_tries))
                 break
 
         x_values = np.linspace(start_region, end_region, num_bins)