# HG changeset patch
# User greg
# Date 1486654129 18000
# Node ID 0f52ca3dfa9c9c0ca9d7e51e15fb6cb0c82af5fd
# Parent  c0a85e845050d9a83f811825533ced44e0e02dde
Uploaded

diff -r c0a85e845050 -r 0f52ca3dfa9c gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 09 10:13:29 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 09 10:28:49 2017 -0500
@@ -14,6 +14,7 @@
     <command>
         <![CDATA[
             #import os
+            #import time
             #set scaffold_path = $scaffold.fields.path
             #set scaffold_dir = $os.path.split($scaffold_path)[0]
             #set scaffold_selection = $os.path.split($scaffold_path)[1]
@@ -104,27 +105,29 @@
                 #end if
             #end if
 
-            && echo $create_ortho_sequences
-            && echo $orthogroups_fasta_src_dir
-            && echo $os.path.exists($orthogroups_fasta_src_dir)
-            && echo $create_corresponding_coding_sequences
-            && echo $orthogroups_fasta_dest_dir
-            && echo $single_copy_orthogroup
-            && echo $single_copy_fasta_src_dir
-            
-            #if $create_ortho_sequences and $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0:
-                #if $create_corresponding_coding_sequences:
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
-                #else:
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
+            #if $create_ortho_sequences:
+                #while not $os.path.exists($orthogroups_fasta_src_dir):
+                    $time.spleep(5)
+                #end while
+                #if len($os.listdir($orthogroups_fasta_src_dir)) > 0:
+                    #if $create_corresponding_coding_sequences:
+                        && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
+                    #else:
+                        && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
+                    #end if
+                    && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
                 #end if
-                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
             #end if
 
             #if $single_copy_orthogroup:
-                #if $create_ortho_sequences and $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0:
-                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
-                    && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
+                #if $create_ortho_sequences:
+                    #while not $os.path.exists($single_copy_fasta_src_dir):
+                        $time.sleep(5)
+                    #end while
+                    #if len($os.listdir($single_copy_fasta_src_dir)) > 0:
+                        && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
+                        && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
+                    #end if
                 #else:
                     && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
                 #end if