working on orthofinder implementation

proost · Jun 14, 2016 · 0b943ce · 0b943ce
1 parent b8db578
commit 0b943ce
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/pipeline/orthology.py b/pipeline/orthology.py
@@ -1,6 +1,6 @@
 import os
 import subprocess
-from shutil import copyfile
+from shutil import copy
 
 from cluster import wait_for_job
 
@@ -26,7 +26,7 @@ def run_orthofinder(self):
                                                          "orthofinder_%d.sh")
 
         for g in self.genomes:
-            copyfile(self.dp[g]['protein_fasta'], os.path.join(orthofinder_dir, g + '.fasta'))
+            copy(self.dp[g]['protein_fasta'], os.path.join(orthofinder_dir, g + '.fasta'))
 
         subprocess.call(["qsub", "-pe", "cores", orthofinder_cores, "-v", "fasta_dir=" + orthofinder_dir + ",num_cores=" + orthofinder_cores, filename])