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1 ##@file SeqStats.py
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2 #
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3 # Utility class to store results (statistics) for a sequence once all coverage results have been processed for it
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4
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5 class SeqStats:
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6 def __init__(self,P_class, P_left, P_right, P_type, P_orient, ave_whole_cov, phage_plus_norm, phage_minus_norm, ArtcohesiveSeq,\
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7 P_seqcoh, Redundant, Mu_like, added_whole_coverage, Permuted, termini_coverage_norm_close, picMaxPlus_norm_close, \
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8 picMaxMinus_norm_close, gen_len, termini_coverage_close,ArtPackmode, termini, forward, reverse, ArtOrient, \
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9 picMaxPlus_close, picMaxMinus_close, picOUT_norm_forw, picOUT_norm_rev, picOUT_forw, picOUT_rev, \
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10 lost_perc, R1, R2, R3, picMaxPlus_host, picMaxMinus_host, drop_cov, added_paired_whole_coverage, P_concat):
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11 self.P_class=P_class # TODO: some information about the meaning of these fields would be welcome.
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12 self.P_left=P_left
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13 self.P_right=P_right
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14 self.P_type=P_type
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15 self.P_orient=P_orient
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16 self.ave_whole_cov=ave_whole_cov
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17 self.phage_plus_norm=phage_plus_norm
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18 self.phage_minus_norm=phage_minus_norm
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19 self.ArtcohesiveSeq=ArtcohesiveSeq
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20 self.P_seqcoh=P_seqcoh
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21 self.Redundant=Redundant
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22 self.Mu_like=Mu_like
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23 self.added_whole_coverage=added_whole_coverage
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24 self.Permuted=Permuted
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25 self.termini_coverage_norm_close=termini_coverage_norm_close
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26 self.picMaxPlus_norm_close=picMaxPlus_norm_close
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27 self.picMaxMinus_norm_close=picMaxMinus_norm_close
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28 self.gen_len=gen_len
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29 self.termini_coverage_close=termini_coverage_close
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30 self.ArtPackmode=ArtPackmode
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31 self.termini=termini
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32 self.forward=forward
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33 self.reverse=reverse
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34 self.ArtOrient=ArtOrient
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35 self.picMaxPlus_close=picMaxPlus_close
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36 self.picMaxMinus_close=picMaxMinus_close
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37 self.picOUT_norm_forw=picOUT_norm_forw
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38 self.picOUT_norm_rev=picOUT_norm_rev
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39 self.picOUT_forw=picOUT_forw
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40 self.picOUT_rev=picOUT_rev
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41 self.lost_perc=lost_perc
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42 self.R1=R1
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43 self.R2=R2
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44 self.R3=R3
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45 self.picMaxPlus_host=picMaxPlus_host
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46 self.picMaxMinus_host=picMaxMinus_host
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47 self.drop_cov=drop_cov
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48 self.added_paired_whole_coverage=added_paired_whole_coverage
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49 self.P_concat=P_concat
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50
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51 def toFile(self,ficname): #TODO: implement me
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52 pass
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53
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54 # types of the elements of the class
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55 # <type 'str'>
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56 # <type 'numpy.int64'>
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57 # <type 'numpy.int64'>
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58 # <type 'str'>
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59 # <type 'str'>
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60 # <type 'float'>
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61 # <class 'pandas.core.frame.DataFrame'>
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62 # <class 'pandas.core.frame.DataFrame'>
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63 # <type 'str'>
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64 # <type 'str'>
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65 # <type 'int'>
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66 # <type 'int'>
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67 # <type 'list'>
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68 # <type 'str'>
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69 # <type 'list'>
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70 # <type 'list'>
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71 # <type 'list'>
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72 # <type 'int'>
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73 # <type 'list'>
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74 # <type 'str'>
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75 # <type 'str'>
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76 # <type 'str'>
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77 # <type 'str'>
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78 # <type 'str'>
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79 # <type 'list'>
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80 # <type 'list'>
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81 # <type 'list'>
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82 # <type 'list'>
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83 # <type 'list'>
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84 # <type 'list'>
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85 # <type 'float'>
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86 # <type 'float'>
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87 # <type 'float'>
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88 # <type 'float'>
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89 # <type 'str'>
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90 # <type 'str'>
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91 # <type 'list'>
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92 # <type 'list'>
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93 # <type 'str'>
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