diff tidy.py @ 0:814eed3d4f3e draft default tip

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/plasmidtron commit d2ae53b6ee23d56d26e9add8fe5ade2e20e75b87-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tidy.py	Thu Apr 11 04:51:28 2019 -0400
@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+
+import sys
+import os
+# from pathlib import Path
+
+
+def make_list(tmp_file, lst_file):
+    dividers = ["_1", "_F", "_R1", "_2", "_R", "_R2"]
+    with open(tmp_file, "r") as fh:
+        lines = fh.readlines()
+        _lines = []
+        processed_list = []
+        for i in range(0,len(lines)):
+            if (os.path.splitext(lines[i].strip())[-1] == ".fasta") or (os.path.splitext(lines[i].strip())[-1] == ".fa"):
+                _lines.append(lines[i].strip())
+            else:
+                file_name = os.path.basename(lines[i])
+                if file_name not in processed_list:
+                    detected_devider = [div for div in dividers if div in file_name]
+                    if len(detected_devider) > 0: 
+                        detected_devider = detected_devider[0]
+                        new_file_name = file_name.split(detected_devider)[0]
+                        for j in range(i+1, len(lines)):
+                            if new_file_name in lines[j]:
+                                paired = "{},{}".format(lines[i].strip(), lines[j].strip())
+                                _lines.append(paired)
+                                processed_list.append(file_name)
+                            # else:
+                            #     _lines.append(lines[i].strip())
+    
+    with open(lst_file,"w") as fh:
+        for _line in _lines:
+            fh.writelines("{}\n".format(_line))
+                    
+if __name__ == "__main__":
+    tmp_file = sys.argv[1]
+    lst_file = sys.argv[2]
+    make_list(tmp_file, lst_file)