diff qualimap_bamqc.py @ 37:407b6a65c867 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

--- a/qualimap_bamqc.py	Thu Jul 26 16:57:57 2018 -0400
+++ b/qualimap_bamqc.py	Fri Jul 27 11:28:26 2018 -0400
@@ -6,8 +6,6 @@
 import shutil
 import sys
 
-OUTPUT_DIR = "qualimap_results"
-
 
 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
     qualimap_command = [
@@ -35,6 +33,8 @@
 
     args = parser.parse_args()
 
+    output_dir = os.path.dirname(args.out_genome_file)
+
     qualimap_bamqc(
         args.input_file,
         args.out_genome_file,
@@ -42,19 +42,24 @@
         args.java_mem_size
     )
 
-    print(os.listdir(os.getcwd()))
-    print(os.listdir(args.out_dir))
+    print(os.listdir(output_dir))
 
-    shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt")
-    shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html")
     shutil.make_archive(
-        './raw_data_qualimapReport',
+        'raw_data_qualimapReport',
         'zip',
         args.out_dir + '/raw_data_qualimapReport'
     )
 
-    print(os.listdir(os.getcwd()))
-    print(os.listdir(args.out_dir))
+    [
+        shutil.move(os.path.join(output_dir, file_name), file_name)
+        for file_name in [
+            "genome_results.txt",
+            "qualimapReport.html",
+            "raw_data_qualimapReport.zip"
+        ]
+    ]
+
+    print(os.listdir(output_dir))
 
 if __name__ == "__main__":
     main()