update to v0.3.6

Author: Jon Palmer

bin/funannotate-predict.py

@@ -713,21 +713,21 @@ def __init__(self,prog):
                 if Transcripts:
                     output.write("TRANSCRIPT\tgenome\t1\n")
             #setup EVM run
-            EVM_out = os.path.join(args.out, 'predict_misc', 'busco.evm.gff3')
+            EVM_busco = os.path.join(args.out, 'predict_misc', 'busco.evm.gff3')
             EVM_script = os.path.join(parentdir, 'bin', 'funannotate-runEVM.py')
             #get absolute paths for everything
             Busco_Weights = os.path.abspath(busco_weights)
-            EVM_out = os.path.abspath(EVM_out)
+            EVM_busco = os.path.abspath(EVM_out)
             Busco_Predictions = os.path.abspath(busco_predictions)
             #parse entire EVM command to script, must be absolute paths for everything
             if Exonerate and Transcripts:
-                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--protein_alignments', os.path.abspath(busco_proteins), '--transcript_alignments', os.path.abspath(busco_transcripts), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), os.path.abspath(EVM_out)]
+                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--protein_alignments', os.path.abspath(busco_proteins), '--transcript_alignments', os.path.abspath(busco_transcripts), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), EVM_busco]
             elif not Exonerate and Transcripts:
-                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'),str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--transcript_alignments', os.path.abspath(busco_transcripts), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), os.path.abspath(EVM_out)]
+                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'),str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--transcript_alignments', os.path.abspath(busco_transcripts), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), EVM_busco]
             elif not Transcripts and Exonerate:
-                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--protein_alignments', os.path.abspath(busco_proteins), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), os.path.abspath(EVM_out)]
+                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--protein_alignments', os.path.abspath(busco_proteins), '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), EVM_busco]
             elif not any([Transcripts,Exonerate]):
-                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), os.path.abspath(EVM_out)]
+                evm_cmd = [sys.executable, EVM_script, os.path.join(args.out, 'logfiles', 'funannotate-EVM_busco.log'), str(args.cpus), '--genome', MaskGenome, '--gene_predictions', Busco_Predictions, '--weights', Busco_Weights, '--min_intron_length', str(args.min_intronlen), EVM_busco]
             #run EVM
             if not os.path.isfile(EVM_out):
                 subprocess.call(evm_cmd)