More changes to support zcat on mac

quatradis/tisp/combine.py

@@ -3,6 +3,7 @@
 """
 import csv
 import os
+import sys
 
 from Bio import bgzf
 
@@ -31,7 +32,9 @@ def prepare_and_create_tabix_for_combined_plots(tabix_plot, combined_dir):
         for line in tabix_plot:
             tabix_plot_fh.write(line + "\n")
 
-    os.system("zcat " + tabix_plot_name + " | sort -k1,1 -k2,2n | bgzip > " + sorted_tabix_plot_name +
+    joiner = " < " if sys.platform == "darwin" else " "
+
+    os.system("zcat" + joiner + tabix_plot_name + " | sort -k1,1 -k2,2n | bgzip > " + sorted_tabix_plot_name +
               " && tabix -b 2 -e 2 " + sorted_tabix_plot_name)
     os.remove(tabix_plot_name)
 

quatradis/tisp/parser.py

@@ -2,6 +2,7 @@
 import os
 import pandas
 import subprocess
+import sys
 
 from Bio import bgzf
 
@@ -133,8 +134,9 @@ def create_file_handle(plot_file, working_dir=""):
     @staticmethod
     def get_plot_file_length(plot_file, working_dir):
         plot_file = working_dir + os.sep + plot_file if working_dir else plot_file
+        joiner = " < " if sys.platform == "darwin" else " "
         cat = "zcat" if plot_file[-3:] == ".gz" else "cat"
-        wc = subprocess.check_output(["bash", "-c", cat + " " + plot_file + " | wc | awk '{print $1}'"])
+        wc = subprocess.check_output(["bash", "-c", cat + joiner + plot_file + " | wc | awk '{print $1}'"])
         file_length = str(wc, 'UTF-8').strip()
         return int(file_length)