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1 #import xlrd #avoid dep
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2 import argparse
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3 import re
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4
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5 parser = argparse.ArgumentParser()
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6 parser.add_argument("--input", help="Excel input file containing one or more sheets where column G has the gene annotation, H has the sequence id and J has the sequence")
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7 parser.add_argument("--ref", help="Reference file")
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8 parser.add_argument("--output", help="Output file")
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9 parser.add_argument("--id", help="ID to be used at the '>>>' line in the output")
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10
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11 args = parser.parse_args()
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12
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13 refdic = dict()
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14 with open(args.ref, 'r') as ref:
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15 currentSeq = ""
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16 currentId = ""
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17 for line in ref:
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18 if line[0] is ">":
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19 if currentSeq is not "" and currentId is not "":
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20 refdic[currentId[1:]] = currentSeq
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21 currentId = line.rstrip()
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22 currentSeq = ""
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23 else:
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24 currentSeq += line.rstrip()
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25 refdic[currentId[1:]] = currentSeq
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26
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27
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28 vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?\*\d{1,2})"]#,
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29 # r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)",
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30 # r"(IGKV[0-3]D?-[0-9]{1,2})",
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31 # r"(IGLV[0-9]-[0-9]{1,2})",
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32 # r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)",
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33 # r"(TRGV[234589])",
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34 # r"(TRDV[1-3])"]
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35
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36 #vPattern = re.compile(r"|".join(vPattern))
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37 vPattern = re.compile("|".join(vPattern))
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38
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39 def filterGene(s, pattern):
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40 if type(s) is not str:
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41 return None
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42 res = pattern.search(s)
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43 if res:
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44 return res.group(0)
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45 return None
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46
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47
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48
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49 currentSeq = ""
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50 currentId = ""
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51 first=True
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52 with open(args.input, 'r') as i:
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53 with open(args.output, 'a') as o:
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54 o.write(">>>" + args.id + "\n")
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55 outputdic = dict()
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56 for line in i:
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57 if first:
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58 first = False
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59 continue
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60 linesplt = line.split("\t")
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61 ref = filterGene(linesplt[1], vPattern)
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62 if not ref or not linesplt[2].rstrip():
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63 continue
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64 if ref in outputdic:
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65 outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
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66 else:
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67 outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]
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68 #print outputdic
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69
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70 for k in outputdic.keys():
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71 if k in refdic:
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72 o.write(">>" + k + "\n")
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73 o.write(refdic[k] + "\n")
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74 for seq in outputdic[k]:
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75 #print seq
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76 o.write(">" + seq[0] + "\n")
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77 o.write(seq[1] + "\n")
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78 else:
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79 print k + " not in reference, skipping " + k
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