Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 15:eca5802b1d6e

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author estrain
date Sat, 07 Sep 2019 12:57:43 -0400
parents 66277925a124
children 81fce62ea8c1
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14:6d28f83c35b1 15:eca5802b1d6e
1218 out, err = salmID_output.communicate() 1218 out, err = salmID_output.communicate()
1219 out=out.decode("utf-8") 1219 out=out.decode("utf-8")
1220 file=open("data_log.txt","a") 1220 file=open("data_log.txt","a")
1221 file.write(out) 1221 file.write(out)
1222 file.close() 1222 file.close()
1223 print("SalmID 1 "+str(out.split("\n")[1]))
1224 print("SalmID 0 "+str(out.split("\n")[0]))
1223 salm_species_scores=out.split("\n")[1].split("\t")[6:] 1225 salm_species_scores=out.split("\n")[1].split("\t")[6:]
1224 salm_species_results=out.split("\n")[0].split("\t")[6:] 1226 salm_species_results=out.split("\n")[0].split("\t")[6:]
1225 max_score=0 1227 max_score=0
1226 max_score_index=1 #default is 1, means "I" 1228 max_score_index=1 #default is 1, means "I"
1227 for i in range(len(salm_species_scores)): 1229 for i in range(len(salm_species_scores)):