Mercurial > repos > charles_s_test > seqsero2

annotate libs/H_combination_output_analysis.py @ 0:6895de35a263 draft

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planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
author charles_s_test
date Thu, 19 Oct 2017 18:16:51 -0400
parents
children 38ad1130d077
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1 #!/usr/bin/env python
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2 # "H_combination_output_analysis.py target.fasta fliCdatabase.fasta fljBdatabase.fasta"
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3 # must have ispcr and primers of fliC and fljB at the same directory
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4
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5
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6 import os
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7 from Bio import SeqIO
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8 import sys
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9 from Bio.Blast import NCBIXML
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10 from Initial_Conditions import phase1
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11 from Initial_Conditions import phase2
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12
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13 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb"
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14 Blastxpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastx"
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15
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16 target=sys.argv[1]
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17 database_fliC=sys.argv[2]
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18 database_fljB=sys.argv[3]
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19 output=target.split('.')[0]+'_out.fasta'
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20
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21 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015
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22 database_path="database"###01/27/2015,database_path=dirpath+"/database"
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23 os.system(dirpath+'/isPcr maxSize=3000 tileSize=7 minPerfect=7 minGood=7 '+target+' '+dirpath+'/../primers/seq_primer_fliC.txt '+target+'_fliC.fa')
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24 os.system(dirpath+'/isPcr maxSize=3000 tileSize=7 minPerfect=7 minGood=7 '+target+' '+dirpath+'/../primers/seq_primer_fljB.txt '+target+'_fljB.fa')
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25 fliC=target+'_fliC.fa'
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26 fljB=target+'_fljB.fa'
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27
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28 if os.path.getsize(fliC)>10:
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29 os.system(Makebltdb+' -in '+database_fliC+' -out '+database_fliC+'_db '+'-dbtype prot')###01/28/2015,no need to add fljB address, because input is abs address already
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30 os.system(Blastxpth+' -seg=no -query '+fliC+' -db '+database_fliC+'_db '+'-out '+'FliC_Htype_'+target+'.xml '+'-outfmt 5')
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31 print target
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32 fliC_XML='FliC_Htype_'+target+'.xml'
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33 fliC_handle=open(fliC_XML)
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34 records=NCBIXML.parse(fliC_handle)
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35 fliC_records=list(records)
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36 E_thresh=1e-10
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37 hspbit=[]
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38 alignmentlist=[]
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39 for record in fliC_records:
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40 for alignment in record.alignments:
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41 hsp_bit_score=0
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42 startlist=[]#the percentage algorithm don't consider one situation, the new hsp cover old hsp
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43 endlist=[]#
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44 for hsp in alignment.hsps:
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45 start=hsp.query_start#
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46 end=hsp.query_end#
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47 leng=abs(start-end)#
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48 if hsp.expect<E_thresh:#
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49 if start>end:#
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50 temp=start#
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51 start=end#
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52 end=start#
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53 if len(startlist)==0:#
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54 hsp_bit_score=hsp_bit_score+hsp.bits#
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55 startlist.append(start)#
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56 endlist.append(end)#
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57 else:#
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58 for i in range(len(startlist)):#
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59 if startlist[i]<start<endlist[i]:#
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60 start=endlist[i]+1#
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61 if startlist[i]<end<endlist[i]:#03112016
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62 end=startlist[i]-1#
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63 if end<start:#the new hsp was included in old hsp#
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64 percentage=0#
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65 else:
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66 percentage=float(end-start)/leng#
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67 startlist.append(start)#
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68 endlist.append(end)#
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69 hsp_bit_score=hsp_bit_score+percentage*hsp.bits#
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70 alignment=alignment.hit_def+':'+str(hsp_bit_score)
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71 hspbit.append(hsp_bit_score)
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72 alignmentlist.append(alignment)
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73 scorelist=dict(zip(alignmentlist,hspbit))
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74 score=0
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75 serotype=[]
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76 seroscore=[]
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77 for Htype in scorelist:
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78 if scorelist[Htype]>score:
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79 First_Choice=Htype
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80 score=scorelist[Htype]
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81 if locals().has_key('First_Choice'):
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82 serotype.append(First_Choice.split("__")[0])
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83 seroscore.append(score)
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84 secscore=0
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85 for Htype in scorelist:
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86
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87 if scorelist[Htype]>secscore and (Htype.split("__")[0] not in serotype):
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88 Sec_Choice=Htype
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89 secscore=scorelist[Htype]
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90 if locals().has_key('Sec_Choice'):
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91 serotype.append(Sec_Choice.split("__")[0])
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92 seroscore.append(secscore)
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93 thirdscore=0
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94 for Htype in scorelist:
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95 if scorelist[Htype]>thirdscore and (Htype.split("__")[0] not in serotype):
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96 Third_Choice=Htype
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97 thirdscore=scorelist[Htype]
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98 if locals().has_key('Third_Choice'):
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99 serotype.append(Third_Choice.split("__")[0])
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100 seroscore.append(thirdscore)
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101 print serotype,seroscore
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102 if score>100:
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103 print '#',target,'$$$ Most possible H_fliC_type: ',First_Choice,'\n'
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104 print '$$$ bit_score:',score,'\n'
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105 if locals().has_key('secscore'):
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106 if secscore>100:
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107 print '#',target,'$$$ Second possible H_fliC_type: ',Sec_Choice,'\n'
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108 print '$$$ Second bit_score:',secscore,'\n'
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109 if locals().has_key('thirdscore'):
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110 if thirdscore>100:
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111 print '#',target,'$$$ Third possible H_fliC_type: ',Third_Choice,'\n'
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112 print '$$$ Third bit_score:',thirdscore,'\n'
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113 else:
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114 print '$$$ No fliC in',target
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115 else:
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116 score=1
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117 print '$$$ No fliC (no file created) in',target
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118
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119
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120
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121 if os.path.getsize(fljB)>10:
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122 os.system(Makebltdb+' -in '+database_fljB+' -out '+database_fljB+'_db '+'-dbtype prot')###01/28/2015,no need to add fljB address, because input is abs address already
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123 os.system(Blastxpth+' -query '+fljB+' -db '+database_fljB+'_db '+'-out '+'FljB_Htype_'+target+'.xml '+'-outfmt 5')
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124 print target
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125 fljB_XML='FljB_Htype_'+target+'.xml'
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126 fljB_handle=open(fljB_XML)
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127 records=NCBIXML.parse(fljB_handle)
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128 fljB_records=list(records)
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129 E_thresh=1e-10
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130 hspbit=[]
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131 alignmentlist=[]
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132 for record in fljB_records:
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133 for alignment in record.alignments:
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134 hsp_bit_score=0
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135 startlist=[]#
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136 endlist=[]#
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137 for hsp in alignment.hsps:
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138 start=hsp.query_start#
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139 end=hsp.query_end#
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140 leng=abs(start-end)#
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141 if hsp.expect<E_thresh:#
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142 if start>end:#
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143 temp=start#
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144 start=end#
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145 end=start#
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146 if len(startlist)==0:#
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147 hsp_bit_score=hsp_bit_score+hsp.bits#
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148 startlist.append(start)#
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149 endlist.append(end)#
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150 else:#
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151 for i in range(len(startlist)):#
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152 if startlist[i]<start<endlist[i]:#
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153 start=endlist[i]+1#
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154 if startlist[i]<end<endlist[i]:#03112016
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155 end=startlist[i]-1#
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156 if end<start:#the new hsp was included in old hsp#
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157 percentage=0#
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158 else:
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159 percentage=float(end-start)/leng#
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160 startlist.append(start)#
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161 endlist.append(end)#
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162 hsp_bit_score=hsp_bit_score+percentage*hsp.bits#
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163 alignment=alignment.hit_def+':'+str(hsp_bit_score)
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164 hspbit.append(hsp_bit_score)
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165 alignmentlist.append(alignment)
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166 fljB_scorelist=dict(zip(alignmentlist,hspbit))
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167
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168 fljB_score=0
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169 fljB_serotype=[]
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170 fljB_seroscore=[]
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171 for Htype in fljB_scorelist:
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172 if fljB_scorelist[Htype]>fljB_score:
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173 fljB_First_Choice=Htype
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174 fljB_score=fljB_scorelist[Htype]
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175 if locals().has_key('fljB_First_Choice'):
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176 fljB_serotype.append(fljB_First_Choice.split("__")[0])
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177 fljB_seroscore.append(fljB_score)
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178 fljB_secscore=0
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179 for Htype in fljB_scorelist:
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180 if fljB_scorelist[Htype]>fljB_secscore and (Htype.split("__")[0] not in fljB_serotype):
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181 fljB_Sec_Choice=Htype
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182 fljB_secscore=fljB_scorelist[Htype]
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183 if locals().has_key('fljB_Sec_Choice'):
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184 fljB_serotype.append(fljB_Sec_Choice.split("__")[0])
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185 fljB_seroscore.append(fljB_secscore)
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186 fljB_thirdscore=0
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187 for Htype in fljB_scorelist:
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188 if fljB_scorelist[Htype]>fljB_thirdscore and (Htype.split("__")[0] not in fljB_serotype):
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189 fljB_Third_Choice=Htype
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190 fljB_thirdscore=fljB_scorelist[Htype]
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191 if locals().has_key('fljB_Third_Choice'):
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192 fljB_serotype.append(fljB_Third_Choice.split("__")[0])
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193 fljB_seroscore.append(fljB_thirdscore)
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194
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195 if fljB_score>100:
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196 print '#',target,'$$$ Most possible H_fljB_type: ',fljB_First_Choice,'\n'
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197 print '$$$ Most bit_score:',fljB_score,'\n'
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198 if locals().has_key('fljB_secscore'):
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199 if fljB_secscore>100:
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200 print '#',target,'$$$ Second possible H_fljB_type: ',fljB_Sec_Choice,'\n'
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201 print '$$$ Second bit_score:',fljB_secscore,'\n'
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202 if locals().has_key('fljB_thirdscore'):
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203 if fljB_thirdscore>100:
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204 print '#',target,'$$$ Third possible H_fljB_type: ',fljB_Third_Choice,'\n'
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205 print '$$$ Third bit_score:',fljB_thirdscore,'\n'
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206 else:
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207 print '$$$ No fljB in',target
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208 else:
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209 fljB_score=1
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210 print '$$$ No fljB (no file created) in',target
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211
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212
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213 if score>100 and fljB_score>100:
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214 fliC_sero=dict(zip(serotype,seroscore))
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215 fljB_sero=dict(zip(fljB_serotype,fljB_seroscore))
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216 combination=[]
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217 combination_score=[]
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218 for seroname in fliC_sero:
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219 for fljB_seroname in fljB_sero:
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220 for i in range(len(phase1)):
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221 if phase1[i]==seroname and phase2[i]==fljB_seroname:
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222 name=seroname+"_"+fljB_seroname
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diff changeset
223 score=fliC_sero[seroname]+fljB_sero[fljB_seroname]
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224 combination.append(name)
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225 combination_score.append(score)
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226 combinationlist=dict(zip(combination,combination_score)) #we can do the filteration here
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227 final_dict=sorted(combinationlist.iteritems(), key=lambda d:d[1], reverse = True)
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228 print "$$_H:Order:",final_dict
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229 elif score>100 and fljB_score<100:
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230 print "$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice
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231 elif score<100 and fljB_score>100:
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232 print "$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice
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233 elif score==1 and fljB_score>100:
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234 print "$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice
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charles_s_test
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235 elif score==1 and fljB_score<100:
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236 print "$$_H:No fliC (file) existed, and no fljB"
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237 elif score>100 and fljB_score==1:
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charles_s_test
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238 print "$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice
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239 elif score<100 and fljB_score==1:
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240 print "$$_H:No fljB (file) existed, and no fliC"
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241 else:
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242 print "$$_H:No fliC and fljB"
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243
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244
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245 '''
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246 E_thresh=1e-10
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247 hspbit=[]
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248 alignmentlist=[]
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249 for record in fliC_records:
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250 for alignment in record.alignments:
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251 hsp_bit_score=0
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252 for hsp in alignment.hsps:
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253 if hsp.expect<E_thresh:
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254 hsp_bit_score=hsp_bit_score+hsp.bits
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255 alignment=alignment.hit_def+':'+str(hsp_bit_score)
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256 hspbit.append(hsp_bit_score)
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257 alignmentlist.append(alignment)
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258
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259 scorelist=dict(zip(alignmentlist,hspbit))
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260 score=0
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261 for Htype in scorelist:
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262 if scorelist[Htype]>score:
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263 First_Choice=Htype
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264 score=scorelist[Htype]
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265 if score>100:
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266 print '#',target,'Most possible H_fliC_type: ',First_Choice,'\n'
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267 print '#bit_score:',score,'\n'
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268 else:
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269 print '#No fliC in',target
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270
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271
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272 E_thresh=1e-10
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273 hspbit=[]
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274 alignmentlist=[]
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275 for record in fljB_records:
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276 for alignment in record.alignments:
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277 hsp_bit_score=0
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278 for hsp in alignment.hsps:
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279 if hsp.expect<E_thresh:
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280 hsp_bit_score=hsp_bit_score+hsp.bits
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281 alignment=alignment.hit_def+':'+str(hsp_bit_score)
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282 hspbit.append(hsp_bit_score)
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283 alignmentlist.append(alignment)
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284
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285 scorelist=dict(zip(alignmentlist,hspbit))
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286 fljB_score=0
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287 for Htype in scorelist:
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288 if scorelist[Htype]>fljB_score:
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289 First_Choice=Htype
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290 fljB_score=scorelist[Htype]
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291 if fljB_score>100:
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292 print '#',target,'Most possible H_fljB_type: ',First_Choice,'\n'
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293 print '#bit_score:',fljB_score,'\n'
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294 else:
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295 print '#No fljB in',target
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296 '''
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297