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1 #!/usr/bin/env
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2
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3 ## Generate basic summary stats for SRST2 (v2) allele score output. Generate summaries for each profile defined in the database
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4 ## author: errol strain, estrain@gmail.com
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5
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6 from argparse import (ArgumentParser, FileType)
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7 import sys
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8 import glob
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9 from decimal import Decimal
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10
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11 def parse_args():
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12 "Parse the input arguments, use '-h' for help."
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13
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14 parser = ArgumentParser(description='Generate Summary Scores for SRST2 Allele Score Output')
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15
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16 # Read inputs
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17 parser.add_argument('--mlst_definitions', type=str, required=True, nargs=1, help='MLST Definitions')
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18 parser.add_argument('--output', type=str, required=True, nargs=1, help='MLST Definitions')
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19 parser.add_argument('--profile_cov', type=str, required=False, help='Minimum Average Coverage to Report ST Profile',default="98")
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20 parser.add_argument('--profile_max_mismatch', type=str, required=False, help='Maximum Number of Mismatches (SNPs)', default="1")
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21
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22 return parser.parse_args()
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23
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24 args =parse_args()
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25
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26 allHash = {}
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27
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28 # Read in Profile Database
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29 profiles = open(args.mlst_definitions[0],"r")
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30 output = open(args.output[0],"w")
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31
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32 # Minimum mean percent coverage for reporting profile
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33 min_per=float(args.profile_cov)
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34 # Maximum mean mismatch for reporting profile
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35 max_mis=float(args.profile_max_mismatch)
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36
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37 # Read in Allele Scores
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38 # Scores should be in srts2*.scores file
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39 # Column 0:Allele, 1:Score, 2:Avg Depth, 5:% Coverage, 7:Mismatches, 8:Indels
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40 scoreFile = open(glob.glob("srst2*.scores")[0],"r")
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41 scoreFile.readline()
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42
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43 for line in scoreFile.readlines() :
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44 els = line.split("\t")
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45 vals = els[0].split("_")
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46 allHash.update({els[0]:line})
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47
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48
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49 # Allele names in first row
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50 als = profiles.readline().rstrip()
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51 filehead = als + str("\tMean_Score\tMean_Depth\tMean_%_Coverage\tTotal_Mismatches\tTotal_Indels\n")
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52 output.write(filehead)
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53
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54 genes = als.split("\t")
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55
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56 for line in profiles.readlines() :
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57 line = line.rstrip()
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58 els = line.split("\t")
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59 alleles = []
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60 for i in range(1,len(genes)) :
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61 alleles.append(genes[i] + "_" + els[i])
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62 mscore=0
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63 mdepth=0
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64 mcover=0
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65 mmisma=0
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66 mindel=0
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67 for i in alleles :
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68 if i in allHash :
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69 vals=str(allHash[i]).split("\t")
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70 mscore+=float(vals[1])
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71 mdepth+=float(vals[2])
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72 mcover+=float(vals[5])
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73 mmisma+=int(vals[7])
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74 mindel+=int(vals[8])
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75
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76 mscore=round(Decimal(mscore/(len(genes)-1)),5)
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77 mdepth=round(Decimal(mdepth/(len(genes)-1)),2)
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78 mcover=round(Decimal(mcover/(len(genes)-1)),2)
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79
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80 if mmisma<=max_mis and mcover>=min_per :
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81 output.write(line + "\t" + str(mscore) + "\t" + str(mdepth) + "\t" + str(mcover) + "\t" + str(mmisma) + "\t" + str(mindel) + "\n")
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82
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