Code clean up

fannyhb · May 10, 2019 · ab972bf · ab972bf
1 parent 86a07f4
commit ab972bf
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/fargene_analysis/fargene_analysis.py b/fargene_analysis/fargene_analysis.py
@@ -151,7 +151,6 @@ def main():
             exit()
     else:
         utils.create_dir(options.out_dir)
-#    outdir = path.abspath(options.out_dir)
 
     for infile in options.infiles:
         if not path.isfile(infile):
@@ -160,12 +159,6 @@ def main():
             logger.info('Exiting pipeline')
             exit()
 
-#    options.hmm_out_dir = '%s/hmmsearchresults' %(outdir)
-#    options.res_dir = '%s/retrievedFragments' %(outdir)
-#    if not options.tmp_dir:
-#        options.tmp_dir = '%s/tmpdir' %(outdir)
-#    options.final_gene_dir = '%s/predictedGenes' %(outdir)
-#    options.assembly_dir = '%s/spades_assembly' %(outdir)
 
     check_arguments(options, logger)
 

diff --git a/fargene_analysis/utils.py b/fargene_analysis/utils.py
@@ -282,7 +282,7 @@ def retrieve_predicted_orfs(options,orfFile):
     aminoOut = '%s/predicted-orfs-amino.fasta' %(abspath(options.final_gene_dir))
     hmmOut = '%s/orfs-%s-hmmsearched.out' %(abspath(options.hmm_out_dir),modelName)
     hitFile = '%s/orfs-positives.out' %(abspath(options.tmp_dir))
-    if isfile(orfFile):
+    if isfile(orfFile) and getsize(orfFile) > 0:
         translate_sequence(orfFile,aminoFile,options,frame)
         perform_hmmsearch(aminoFile,options.hmm_model,hmmOut,options)
         hitDict = orf_classifier(hmmOut,hitFile,options)
@@ -292,6 +292,7 @@ def retrieve_predicted_orfs(options,orfFile):
         return fastaOut
     else:
         logging.error('The file %s does not exist' %(orfFile))
+        return fastaOut
 
 def orf_classifier(hmmOut,hitFile,options):
     threshold = "$14>%s" %(options.long_score)