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1 import re
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2
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3 #------------------------------------------------------------------------------
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4
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5 class Profiles:
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6 '''
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7 Hmm profile Class
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8 Attributes are name, desc, length, accNumber, GA_cut_off and retrieve
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9 '''
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10
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11 #--------------------------------------------------------------------------
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12
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13 def __init__( self, name="", desc="", length=0, accNumber = "", GA_cut_off = 0, retrieve = False ):
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14 self.name = name
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15 self.desc = desc
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16 self.length = length
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17 self.accNumber = accNumber
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18 self.GA_cut_off = GA_cut_off
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19 self.retrieve = retrieve
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20 self.tab_profile = []
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21
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22 #--------------------------------------------------------------------------
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23
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24 def _noProfileInFile(self):
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25 self.name = None
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26 self.desc = None
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27 self.length = None
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28 self.accNumber = None
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29 self.GA_cut_off = None
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30
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31 #--------------------------------------------------------------------------
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32
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33 def _initialisation(self):
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34 self.name = ""
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35 self.desc = ""
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36 self.length = 0
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37 self.accNumber = ""
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38 GA_cut_off = 0
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39 self.tab_profile = []
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40
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41 #--------------------------------------------------------------------------
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42
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43 def read( self, hmmFile ):
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44 '''
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45 Read a profile and characterize the object profile
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46 attributes name, length, desc, accNumber and GA_cut_off are specified
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47 '''
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48 line = hmmFile.readline()
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49 if line == "":
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50 self._noProfileInFile()
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51 return
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52 self._initialisation()
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53 if self.retrieve:
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54 self.tab_profile.append(line)
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55 while not re.match("\/\/.*", line):
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56 line = hmmFile.readline()
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57 if self.retrieve:
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58 self.tab_profile.append(line)
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59 name = re.match("NAME\s*(.*)", line)
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60 if name:
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61 self.name = name.group(1)
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62 desc = re.match("DESC\s*(.*)", line)
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63 if desc:
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64 self.desc = desc.group(1)
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65 length = re.match("LENG\s*(.*)", line)
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66 if length:
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67 self.length = int(length.group(1))
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68 accNumber = re.match("ACC\s*(.*)", line)
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69 if accNumber:
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70 self.accNumber = accNumber.group(1)
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71 GA_cut_off = re.match("GA\s*\d*\.\d*\s*(.*);", line)
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72 if GA_cut_off:
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73 self.GA_cut_off = float(GA_cut_off.group(1))
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74 else :
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75 if (self.GA_cut_off == 0):
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76 self.GA_cut_off = "NA"
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77 if self.retrieve:
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78 return self.tab_profile
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79 else:
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80 return 1
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81
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82 #--------------------------------------------------------------------------
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83
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84 def readAndRetrieve( self, hmmFile ):
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85 '''
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86 Read a profile and characterize the object profile
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87 attributes name, length, desc, accNumber and GA_cut_off are specified
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88 And a list of each line of profile is returned
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89 '''
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90 self.retrieve = True
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91 return self.read(hmmFile)
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