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1 import re
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2 import argparse
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3
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4 parser = argparse.ArgumentParser()
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5 parser.add_argument("--mutationfile", help="The '7_V-REGION-mutation-and-AA-change-table' file from the IMGT output")
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6 parser.add_argument("--hotspotfile", help="The '10_V-REGION-mutation-hotspots' file from the IMGT output")
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7 parser.add_argument("--output", help="Output file")
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8
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9 args = parser.parse_args()
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10
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11 mutationfile = args.mutationfile #"test_VH-Ca_Cg_25nt/7_V-REGION-mutation-and-AA-change-table_test_VH-Ca_Cg_25nt_241013.txt"
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12 hotspotsfile = args.hotspotfile #"test_VH-Ca_Cg_25nt/10_V-REGION-mutation-hotspots_test_VH-Ca_Cg_25nt_241013.txt"
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13 outfile = args.output #"out.txt"
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14
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15 mutationdic = dict()
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16 mutationMatcher = re.compile("^(.)(\d+).(.),?(.)?(\d+)?.?(.)?(.?.?.?.?.?)?")
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17 linecount = 0
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18
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19 with open(mutationfile, 'r') as i:
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20 for line in i.readlines()[1:]:
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21 linecount += 1
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22 linesplt = line.split("\t")
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23 if linesplt[2] != "productive":
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24 continue
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25 ID = linesplt[1]
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26 mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[5].split("|") if x]
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27 mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[6].split("|") if x]
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28 mutationdic[ID + "_FR2"] = [mutationMatcher.match(x).groups() for x in linesplt[7].split("|") if x]
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29 mutationdic[ID + "_CDR2"] = [mutationMatcher.match(x).groups() for x in linesplt[8].split("|") if x]
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30 mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"]
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31 mutationdic[ID + "_FR3"] = [mutationMatcher.match(x).groups() for x in linesplt[9].split("|") if x]
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32
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33 if linecount == 0:
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34 print "No data, exiting"
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35 with open(outfile, 'w') as o:
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36 o.write("RGYW (%),0,0,NA\n")
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37 o.write("WRCY (%),0,0,NA\n")
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38 o.write("WA (%),0,0,NA\n")
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39 o.write("TW (%),0,0,NA\n")
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40 import sys
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41 sys.exit()
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42
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43 hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
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44 RGYWCount = 0
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45 WRCYCount = 0
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46 WACount = 0
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47 TWCount = 0
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48
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49 with open(hotspotsfile, 'r') as i:
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50 for line in i.readlines()[1:]:
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51 linesplt = line.split("\t")
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52 if linesplt[2] != "productive":
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53 continue
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54 ID = linesplt[1]
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55 RGYW = [(int(x),int(y),z) for (x,y,z) in [hotspotMatcher.match(x).groups() for x in linesplt[6].split("|") if x]]
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56 WRCY = [(int(x),int(y),z) for (x,y,z) in [hotspotMatcher.match(x).groups() for x in linesplt[7].split("|") if x]]
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57 WA = [(int(x),int(y),z) for (x,y,z) in [hotspotMatcher.match(x).groups() for x in linesplt[4].split("|") if x]]
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58 TW = [(int(x),int(y),z) for (x,y,z) in [hotspotMatcher.match(x).groups() for x in linesplt[5].split("|") if x]]
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59 RGYWCount += sum([1 for (x,y,z) in RGYW if z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
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60 WRCYCount += sum([1 for (x,y,z) in WRCY if z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
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61 WACount += sum([1 for (x,y,z) in WA if z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
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62 TWCount += sum([1 for (x,y,z) in TW if z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
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63
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64 path = outfile[:outfile.rfind("/") + 1] + "mutations.txt"
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65 value = 0;
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66 with open(path, 'r') as f:
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67 value = f.readlines()[0].split(",")[1]
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68 with open(outfile, 'w') as o:
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69 if value != "0":
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70 o.write("RGYW (%)," + str(RGYWCount) + "," + value + "," + str(round(RGYWCount / float(value) * 100, 1)) + "\n")
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71 o.write("WRCY (%)," + str(WRCYCount) + "," + value + "," + str(round(WRCYCount / float(value) * 100, 1)) + "\n")
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72 o.write("WA (%)," + str(WACount) + "," + value + "," + str(round(WACount / float(value) * 100, 1)) + "\n")
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73 o.write("TW (%)," + str(TWCount) + "," + value + "," + str(round(TWCount / float(value) * 100, 1)) + "\n")
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74 else:
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75 o.write("RGYW (%)," + str(RGYWCount) + ",0,NA\n")
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76 o.write("WRCY (%)," + str(WRCYCount) + ",0,NA\n")
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77 o.write("WA (%)," + str(WACount) + ",0,NA\n")
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78 o.write("TW (%)," + str(TWCount) + ",0,NA\n")
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79
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80
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