Mercurial > repos > jpayne > seqsero_v2

comparison 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
comparison
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8:77d3edd25de7 9:eefafc531698
1310 predicted_antigenic_profile = predict_form, 1310 predicted_antigenic_profile = predict_form,
1311 predicted_subspecies = subspecies, 1311 predicted_subspecies = subspecies,
1312 predicted_serotype = "{}{}".format(predict_sero, star), 1312 predicted_serotype = "{}{}".format(predict_sero, star),
1313 note=claim.replace('\n','') 1313 note=claim.replace('\n','')
1314 ) 1314 )
1315 result['*'] = star_line.replace('\t', ' ') 1315 result['*'] = star_line.replace('\t', ' ').replace('\n','')
1316 with open("Seqsero_result.tsv","w") as new_file: 1316 with open("Seqsero_result.tsv","w") as new_file:
1317 #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")#+## 1317 #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")#+##
1318 #new_file.close() 1318 #new_file.close()
1319 wrtr = DictWriter(new_file, delimiter='\t', fieldnames=result.keys()) 1319 wrtr = DictWriter(new_file, delimiter='\t', fieldnames=result.keys())
1320 wrtr.writeheader() 1320 wrtr.writeheader()
1368 predicted_antigenic_profile = predict_form, 1368 predicted_antigenic_profile = predict_form,
1369 predicted_subspecies = subspecies, 1369 predicted_subspecies = subspecies,
1370 predicted_serotype = "{}{}".format(predict_sero, star), 1370 predicted_serotype = "{}{}".format(predict_sero, star),
1371 note=claim.replace('\n','') 1371 note=claim.replace('\n','')
1372 ) 1372 )
1373 result['*'] = star_line.replace('\t', ' ') 1373 result['*'] = star_line.replace('\t', ' ').replace('\n','')
1374 with open("Seqsero_result.tsv","w") as new_file: 1374 with open("Seqsero_result.tsv","w") as new_file:
1375 #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")#+## 1375 #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")#+##
1376 #new_file.close() 1376 #new_file.close()
1377 wrtr = DictWriter(new_file, delimiter='\t', fieldnames=result.keys()) 1377 wrtr = DictWriter(new_file, delimiter='\t', fieldnames=result.keys())
1378 wrtr.writeheader() 1378 wrtr.writeheader()