Mercurial > repos > jpayne > seqsero_v2

diff SeqSero2/SeqSero2_package.py @ 9:eefafc531698

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planemo upload
author jpayne
date Fri, 07 Jun 2019 16:24:18 -0400
parents 77d3edd25de7
children 4ac593d4b40f
line wrap: on
line diff
--- a/SeqSero2/SeqSero2_package.py	Fri Jun 07 16:16:25 2019 -0400
+++ b/SeqSero2/SeqSero2_package.py	Fri Jun 07 16:24:18 2019 -0400
@@ -1312,7 +1312,7 @@
           predicted_serotype = "{}{}".format(predict_sero, star),
           note=claim.replace('\n','')
           )
-          result['*'] = star_line.replace('\t', ' ')
+          result['*'] = star_line.replace('\t', ' ').replace('\n','')
           with open("Seqsero_result.tsv","w") as new_file:
          #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
          #new_file.close()
@@ -1370,7 +1370,7 @@
           predicted_serotype = "{}{}".format(predict_sero, star),
           note=claim.replace('\n','')
         )
-        result['*'] = star_line.replace('\t', ' ')
+        result['*'] = star_line.replace('\t', ' ').replace('\n','')
         with open("Seqsero_result.tsv","w") as new_file:
          #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
          #new_file.close()