Mercurial > repos > cstrittmatter > seqsero_v2

annotate libs/mapping_and_assembly_hybrid.py @ 1:3b30ea175c54 draft default tip

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author cstrittmatter
date Thu, 21 Dec 2017 12:48:10 -0500
parents 6275272ebcbc
children
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1 import os,sys,glob,time,itertools,subprocess
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2 from Initial_Conditions import phase1
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3 from Initial_Conditions import phase2
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4 from Initial_Conditions import phaseO
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5 from Initial_Conditions import sero
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6 from distutils.version import LooseVersion
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7
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11 def xml_parse_score_comparision_seqsero(xmlfile):
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12 #used to do seqsero xml analysis
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13 from Bio.Blast import NCBIXML
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14 handle=open(xmlfile)
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15 handle=NCBIXML.parse(handle)
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16 handle=list(handle)
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17 List=[]
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18 List_score=[]
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19 List_ids=[]
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20 for i in range(len(handle)):
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21 if len(handle[i].alignments)>0:
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22 for j in range(len(handle[i].alignments)):
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23 score=0
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24 ids=0
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25 List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def)
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26 for z in range(len(handle[i].alignments[j].hsps)):
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27 if "last" in handle[i].query or "first" in handle[i].query:
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28 score+=handle[i].alignments[j].hsps[z].bits
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29 ids+=float(handle[i].alignments[j].hsps[z].identities)/handle[i].query_length
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30 else:
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31 if handle[i].alignments[j].hsps[z].align_length>=30:
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32 #for the long alleles, filter noise parts
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33 score+=handle[i].alignments[j].hsps[z].bits
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34 ids+=float(handle[i].alignments[j].hsps[z].identities)/handle[i].query_length
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35 List_score.append(score)
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36 List_ids.append(ids)
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37 temp=zip(List,List_score,List_ids)
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38 Final_list=sorted(temp, key=lambda d:d[1], reverse = True)
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39 return Final_list
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40
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41
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42 def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number
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43 Old=L
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44 L.sort()
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45 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
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46 count=[]
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47 for j in range(len(L)):
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48 y=0
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49 for x in Old:
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50 if L[j]==x:
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51 y+=1
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52 count.append(y)
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53 if sort_on_fre!="none":
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54 d=zip(*sorted(zip(count, L)))
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55 L=d[1]
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56 count=d[0]
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57 return (L,count)
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58
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59
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60 def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list):
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61 #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test
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62 #this is mainly used for
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63 a=nodes_vs_score_list
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64 fliC_score=0
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65 fljB_score=0
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66 for z in a:
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67 if "fliC" in z[0]:
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68 fliC_score+=z[1]
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69 elif "fljB" in z[0]:
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70 fljB_score+=z[1]
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71 if fliC_score>=fljB_score:
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72 role="fliC"
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73 else:
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74 role="fljB"
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75 return (role,abs(fliC_score-fljB_score))
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76
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77 def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list_passed):
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78 #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small)
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79 #also used when no head or tail got blasted score for the contig
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80 role=""
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81 for z in Final_list_passed:
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82 if node_name in z[0]:
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83 role=z[0].split("_")[0]
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84 break
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85 return role
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86
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87
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88 def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list_passed):
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89 #nodes_list is the c created by c,d=Uniq(nodes) in below function
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90 first_target=""
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91 role_list=[]
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92 for x in nodes_list:
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93 a=[]
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94 role=""
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95 for y in tail_head_list:
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96 if x in y[0]:
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97 a.append(y)
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98 if len(a)==4:
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99 #compare two heads (37 > 30)
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100 #four contigs, most perfect assembly, high quality
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101 """
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102 for z in a:
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103 if "fliC_first_37" in z[0]:
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104 t1=z[1]
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105 elif "fljB_first_37" in z[0]:
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106 t2=z[1]
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107 if t1>=t2:
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108 role="fliC"
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109 else:
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110 role="fljB"
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111 """
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112 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
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113 if diff<20:
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114 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
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115 elif len(a)==3:
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116 """
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117 #compare the number, because hybrid problem
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118 temp=[]
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119 for z in a:
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120 temp.append(z[0].split("_")[0])
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121 m,n=Uniq(temp)#only two choices in m or n
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122 if n[0]>n[1]:
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123 role=m[0]
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124 else:
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125 role=m[1]
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126 """
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127 ###however, if the one with highest score is the fewer one, compare their accumulation score
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128 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
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129 if diff<20:
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130 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
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131 ###end of above score comparison
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132 elif len(a)==2:
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133 #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37)
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134 temp=[]
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135 for z in a:
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136 temp.append(z[0].split("_")[0])
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137 m,n=Uniq(temp)#should only have one choice, but weird situation might occur too
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138 if len(m)==1:
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139 pass
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140 else:
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141 pass
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142 #print "head and tail not belong to same role, now let's guess based on maximum likelihood"
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143 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
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144 if diff<20:
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145 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
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146 """
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147 max_unit_score=0
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148 for z in a:
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149 unit_score=z[-1]/int(z[0].split("__")[1])
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150 if unit_score>=max_unit_score:
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151 role=z[0].split("_")[0]
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152 max_unit_score=unit_score
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153 """
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154 ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation
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155 elif len(a)==1:
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156 #that one
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157 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
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158 if diff<20:
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159 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
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160 #role=a[0][0].split("_")[0]
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161 #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0"
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162 else:#a==0
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163 #use Final_list_passed best match
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164 for z in Final_list_passed:
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165 if x in z[0]:
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166 role=z[0].split("_")[0]
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167 break
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168 #print x,role,len(a)
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169 role_list.append((role,x))
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170 if len(role_list)==2:
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171 if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase
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172 #just use score to do a final test
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173 role_list=[]
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174 for x in nodes_list:
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175 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
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176 role_list.append((role,x))
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177 return role_list
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178
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179 def decide_contig_roles_for_H_antigen(Final_list):
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180 #used to decide which contig is FliC and which one is fljB
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181 contigs=[]
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182 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
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183 nodes=[]
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184 for x in Final_list_passed:
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185 if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]:
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186 nodes.append(x[0].split("___")[1].strip())
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187 c,d=Uniq(nodes)#c is node_list
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188 #print c
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189 tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])]
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190 roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list_passed)
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191 return roles
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192
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193 def Combine(b,c):
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194 fliC_combinations=[]
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195 fliC_combinations.append(",".join(c))
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196 temp_combinations=[]
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197 for i in range(len(b)):
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198 for x in itertools.combinations(b,i+1):
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199 temp_combinations.append(",".join(x))
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200 for x in temp_combinations:
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201 temp=[]
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202 for y in c:
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203 temp.append(y)
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204 temp.append(x)
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205 temp=",".join(temp)
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206 temp=temp.split(",")
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207 temp.sort()
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208 temp=",".join(temp)
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209 fliC_combinations.append(temp)
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210 return fliC_combinations
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211
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212 def decide_O_type_and_get_special_genes(Final_list):
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213 #decide O based on Final_list
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214 O_choice="?"
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215 O_list=[]
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216 special_genes=[]
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217 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
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218 nodes=[]
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219 for x in Final_list_passed:
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220 if x[0].startswith("O-"):
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221 nodes.append(x[0].split("___")[1].strip())
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222 elif not x[0].startswith("fl"):
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223 special_genes.append(x)
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224 #print "special_genes:",special_genes
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225 c,d=Uniq(nodes)
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226 #print "potential O antigen contig",c
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227 final_O=[]
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228 O_nodes_list=[]
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229 for x in c:#c is the list for contigs
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230 temp=0
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231 for y in Final_list_passed:
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232 if x in y[0] and y[0].startswith("O-"):
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233 final_O.append(y)
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diff changeset
234 break
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cstrittmatter
parents:
diff changeset
235 ### O contig has the problem of two genes on same contig, so do additional test
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cstrittmatter
parents:
diff changeset
236 potenial_new_gene=""
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cstrittmatter
parents:
diff changeset
237 for x in final_O:
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cstrittmatter
parents:
diff changeset
238 pointer=0 #for genes merged or not
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cstrittmatter
parents:
diff changeset
239 #not consider O-1,3,19_not_in_3,10, too short compared with others
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cstrittmatter
parents:
diff changeset
240 if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])+800 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region
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cstrittmatter
parents:
diff changeset
241 pointer=x[0].split("___")[1].strip()#store the contig name
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cstrittmatter
parents:
diff changeset
242 print pointer
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cstrittmatter
parents:
diff changeset
243 if pointer!=0:#it has potential merge event
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cstrittmatter
parents:
diff changeset
244 for y in Final_list:
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cstrittmatter
parents:
diff changeset
245 if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O
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cstrittmatter
parents:
diff changeset
246 potenial_new_gene=y
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cstrittmatter
parents:
diff changeset
247 print potenial_new_gene
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cstrittmatter
parents:
diff changeset
248 break
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cstrittmatter
parents:
diff changeset
249 if potenial_new_gene!="":
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cstrittmatter
parents:
diff changeset
250 print "two differnt genes in same contig, fix it for O antigen"
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cstrittmatter
parents:
diff changeset
251 final_O.append(potenial_new_gene)
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cstrittmatter
parents:
diff changeset
252 ### end of the two genes on same contig test
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cstrittmatter
parents:
diff changeset
253 if len(final_O)==0:
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cstrittmatter
parents:
diff changeset
254 #print "$$$No Otype, due to no hit"#may need to be changed
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cstrittmatter
parents:
diff changeset
255 O_choice="-"
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cstrittmatter
parents:
diff changeset
256 else:
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cstrittmatter
parents:
diff changeset
257 O_list=[]
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cstrittmatter
parents:
diff changeset
258 for x in final_O:
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cstrittmatter
parents:
diff changeset
259 O_list.append(x[0].split("__")[0])
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cstrittmatter
parents:
diff changeset
260 if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis
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cstrittmatter
parents:
diff changeset
261 O_nodes_list.append(x[0].split("___")[1])
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cstrittmatter
parents:
diff changeset
262 ### special test for O9,46 and O3,10 family
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cstrittmatter
parents:
diff changeset
263 if "O-9,46_wbaV" in O_list:#not sure should use and float(O9_wbaV)/float(num_1) > 0.1
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cstrittmatter
parents:
diff changeset
264 if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1
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cstrittmatter
parents:
diff changeset
265 O_choice="O-9,46"
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cstrittmatter
parents:
diff changeset
266 #print "$$$Most possilble Otype: O-9,46"
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cstrittmatter
parents:
diff changeset
267 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
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cstrittmatter
parents:
diff changeset
268 O_choice="O-9,46,27"
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cstrittmatter
parents:
diff changeset
269 #print "$$$Most possilble Otype: O-9,46,27"
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cstrittmatter
parents:
diff changeset
270 else:
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cstrittmatter
parents:
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271 O_choice="O-9"#next, detect O9 vs O2?
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cstrittmatter
parents:
diff changeset
272 O2=0
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cstrittmatter
parents:
diff changeset
273 O9=0
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cstrittmatter
parents:
diff changeset
274 for z in special_genes:
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cstrittmatter
parents:
diff changeset
275 if "tyr-O-9" in z[0]:
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cstrittmatter
parents:
diff changeset
276 O9=z[1]
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cstrittmatter
parents:
diff changeset
277 elif "tyr-O-2" in z[0]:
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cstrittmatter
parents:
diff changeset
278 O2=z[1]
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cstrittmatter
parents:
diff changeset
279 if O2>O9:
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cstrittmatter
parents:
diff changeset
280 O_choice="O-2"
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cstrittmatter
parents:
diff changeset
281 elif O2<O9:
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cstrittmatter
parents:
diff changeset
282 pass
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cstrittmatter
parents:
diff changeset
283 else:
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cstrittmatter
parents:
diff changeset
284 pass
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cstrittmatter
parents:
diff changeset
285 #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility."
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cstrittmatter
parents:
diff changeset
286 elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1
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cstrittmatter
parents:
diff changeset
287 if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1
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cstrittmatter
parents:
diff changeset
288 O_choice="O-3,10"
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cstrittmatter
parents:
diff changeset
289 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
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cstrittmatter
parents:
diff changeset
290 else:
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cstrittmatter
parents:
diff changeset
291 O_choice="O-1,3,19"
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cstrittmatter
parents:
diff changeset
292 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
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cstrittmatter
parents:
diff changeset
293 ### end of special test for O9,46 and O3,10 family
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cstrittmatter
parents:
diff changeset
294 else:
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cstrittmatter
parents:
diff changeset
295 try:
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cstrittmatter
parents:
diff changeset
296 max_score=0
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cstrittmatter
parents:
diff changeset
297 for x in final_O:
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cstrittmatter
parents:
diff changeset
298 if x[1]>=max_score:
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cstrittmatter
parents:
diff changeset
299 max_score=x[1]
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cstrittmatter
parents:
diff changeset
300 O_choice=x[0].split("_")[0]
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cstrittmatter
parents:
diff changeset
301 if O_choice=="O-1,3,19":
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cstrittmatter
parents:
diff changeset
302 O_choice=final_O[1][0].split("_")[0]
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cstrittmatter
parents:
diff changeset
303 #print "$$$Most possilble Otype: ",O_choice
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cstrittmatter
parents:
diff changeset
304 except:
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cstrittmatter
parents:
diff changeset
305 pass
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cstrittmatter
parents:
diff changeset
306 #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
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cstrittmatter
parents:
diff changeset
307 #print "O:",O_choice,O_nodes_list
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cstrittmatter
parents:
diff changeset
308 return O_choice,O_nodes_list,special_genes,final_O
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cstrittmatter
parents:
diff changeset
309
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cstrittmatter
parents:
diff changeset
310 def seqsero_from_formula_to_serotypes(Otype,fliC,fljB,special_gene_list):
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cstrittmatter
parents:
diff changeset
311 #like test_output_06012017.txt
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cstrittmatter
parents:
diff changeset
312 #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list)
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cstrittmatter
parents:
diff changeset
313 from Initial_Conditions import phase1
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cstrittmatter
parents:
diff changeset
314 from Initial_Conditions import phase2
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cstrittmatter
parents:
diff changeset
315 from Initial_Conditions import phaseO
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cstrittmatter
parents:
diff changeset
316 from Initial_Conditions import sero
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cstrittmatter
parents:
diff changeset
317 seronames=[]
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cstrittmatter
parents:
diff changeset
318 for i in range(len(phase1)):
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cstrittmatter
parents:
diff changeset
319 fliC_combine=[]
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cstrittmatter
parents:
diff changeset
320 fljB_combine=[]
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cstrittmatter
parents:
diff changeset
321 if phaseO[i]==Otype:
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cstrittmatter
parents:
diff changeset
322 ### for fliC, detect every possible combinations to avoid the effect of "["
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cstrittmatter
parents:
diff changeset
323 if phase1[i].count("[")==0:
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cstrittmatter
parents:
diff changeset
324 fliC_combine.append(phase1[i])
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cstrittmatter
parents:
diff changeset
325 elif phase1[i].count("[")>=1:
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cstrittmatter
parents:
diff changeset
326 c=[]
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cstrittmatter
parents:
diff changeset
327 b=[]
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cstrittmatter
parents:
diff changeset
328 if phase1[i][0]=="[" and phase1[i][-1]=="]" and phase1[i].count("[")==1:
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cstrittmatter
parents:
diff changeset
329 content=phase1[i].replace("[","").replace("]","")
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cstrittmatter
parents:
diff changeset
330 fliC_combine.append(content)
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cstrittmatter
parents:
diff changeset
331 fliC_combine.append("-")
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cstrittmatter
parents:
diff changeset
332 else:
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cstrittmatter
parents:
diff changeset
333 for x in phase1[i].split(","):
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cstrittmatter
parents:
diff changeset
334 if "[" in x:
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cstrittmatter
parents:
diff changeset
335 b.append(x.replace("[","").replace("]",""))
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cstrittmatter
parents:
diff changeset
336 else:
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cstrittmatter
parents:
diff changeset
337 c.append(x)
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cstrittmatter
parents:
diff changeset
338 fliC_combine=Combine(b,c) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t
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cstrittmatter
parents:
diff changeset
339 ### end of fliC "[" detect
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cstrittmatter
parents:
diff changeset
340 ### for fljB, detect every possible combinations to avoid the effect of "["
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cstrittmatter
parents:
diff changeset
341 if phase2[i].count("[")==0:
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cstrittmatter
parents:
diff changeset
342 fljB_combine.append(phase2[i])
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cstrittmatter
parents:
diff changeset
343 elif phase2[i].count("[")>=1:
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cstrittmatter
parents:
diff changeset
344 d=[]
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cstrittmatter
parents:
diff changeset
345 e=[]
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cstrittmatter
parents:
diff changeset
346 if phase2[i][0]=="[" and phase2[i][-1]=="]" and phase2[i].count("[")==1:
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cstrittmatter
parents:
diff changeset
347 content=phase2[i].replace("[","").replace("]","")
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cstrittmatter
parents:
diff changeset
348 fljB_combine.append(content)
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cstrittmatter
parents:
diff changeset
349 fljB_combine.append("-")
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cstrittmatter
parents:
diff changeset
350 else:
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cstrittmatter
parents:
diff changeset
351 for x in phase2[i].split(","):
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cstrittmatter
parents:
diff changeset
352 if "[" in x:
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cstrittmatter
parents:
diff changeset
353 d.append(x.replace("[","").replace("]",""))
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cstrittmatter
parents:
diff changeset
354 else:
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cstrittmatter
parents:
diff changeset
355 e.append(x)
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cstrittmatter
parents:
diff changeset
356 fljB_combine=Combine(d,e)
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cstrittmatter
parents:
diff changeset
357 ### end of fljB "[" detect
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cstrittmatter
parents:
diff changeset
358 new_fliC=fliC.split(",") #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings
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cstrittmatter
parents:
diff changeset
359 new_fliC.sort()
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cstrittmatter
parents:
diff changeset
360 new_fliC=",".join(new_fliC)
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cstrittmatter
parents:
diff changeset
361 new_fljB=fljB.split(",")
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cstrittmatter
parents:
diff changeset
362 new_fljB.sort()
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cstrittmatter
parents:
diff changeset
363 new_fljB=",".join(new_fljB)
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cstrittmatter
parents:
diff changeset
364 if (new_fliC in fliC_combine or fliC in fliC_combine) and (new_fljB in fljB_combine or fljB in fljB_combine):
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cstrittmatter
parents:
diff changeset
365 seronames.append(sero[i])
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cstrittmatter
parents:
diff changeset
366 #analyze seronames
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cstrittmatter
parents:
diff changeset
367 if len(seronames)==0:
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cstrittmatter
parents:
diff changeset
368 seronames=["N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"]
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cstrittmatter
parents:
diff changeset
369 star=""
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cstrittmatter
parents:
diff changeset
370 star_line=""
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cstrittmatter
parents:
diff changeset
371 if len(seronames)>1:#there are two possible predictions for serotypes
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cstrittmatter
parents:
diff changeset
372 star="*"
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cstrittmatter
parents:
diff changeset
373 star_line="The predicted serotypes share the same general formula:\t"+Otype+":"+fliC+":"+fljB+"\n"##
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cstrittmatter
parents:
diff changeset
374 print "\n"
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cstrittmatter
parents:
diff changeset
375 predict_form=Otype+":"+fliC+":"+fljB#
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cstrittmatter
parents:
diff changeset
376 predict_sero=(" or ").join(seronames)
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cstrittmatter
parents:
diff changeset
377 ###special test for Enteritidis
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cstrittmatter
parents:
diff changeset
378 if predict_form=="9:g,m:-":
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cstrittmatter
parents:
diff changeset
379 sdf="-"
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cstrittmatter
parents:
diff changeset
380 for x in special_gene_list:
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cstrittmatter
parents:
diff changeset
381 if x[0].startswith("sdf"):
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cstrittmatter
parents:
diff changeset
382 sdf="+"
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cstrittmatter
parents:
diff changeset
383 predict_form=predict_form+"\nSdf prediction:"+sdf
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cstrittmatter
parents:
diff changeset
384 if sdf=="-":
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cstrittmatter
parents:
diff changeset
385 star="*"
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cstrittmatter
parents:
diff changeset
386 star_line="Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n"#+##
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cstrittmatter
parents:
diff changeset
387 predict_sero="See comments below"
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cstrittmatter
parents:
diff changeset
388 ###end of special test for Enteritidis
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cstrittmatter
parents:
diff changeset
389 elif predict_form=="4:i:-":
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cstrittmatter
parents:
diff changeset
390 predict_sero="potential monophasic variant of Typhimurium"
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cstrittmatter
parents:
diff changeset
391 elif predict_form=="4:r:-":
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cstrittmatter
parents:
diff changeset
392 predict_sero="potential monophasic variant of Heidelberg"
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cstrittmatter
parents:
diff changeset
393 elif predict_form=="4:b:-":
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cstrittmatter
parents:
diff changeset
394 predict_sero="potential monophasic variant of Paratyphi B"
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cstrittmatter
parents:
diff changeset
395 elif predict_form=="8:e,h:1,2":
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cstrittmatter
parents:
diff changeset
396 predict_sero="Newport"
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cstrittmatter
parents:
diff changeset
397 star="*"
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cstrittmatter
parents:
diff changeset
398 star_line="Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."
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cstrittmatter
parents:
diff changeset
399 claim="The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes."##
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cstrittmatter
parents:
diff changeset
400 if "N/A" in predict_sero:
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cstrittmatter
parents:
diff changeset
401 claim=""
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cstrittmatter
parents:
diff changeset
402 if "Typhimurium" in predict_sero or predict_form=="4:i:-":
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cstrittmatter
parents:
diff changeset
403 normal=0
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cstrittmatter
parents:
diff changeset
404 mutation=0
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cstrittmatter
parents:
diff changeset
405 for x in special_gene_list:
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cstrittmatter
parents:
diff changeset
406 if "oafA-O-4_full" in x[0]:
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cstrittmatter
parents:
diff changeset
407 normal=x[1]
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cstrittmatter
parents:
diff changeset
408 elif "oafA-O-4_5-" in x[0]:
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cstrittmatter
parents:
diff changeset
409 mutation=x[1]
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cstrittmatter
parents:
diff changeset
410 if normal>mutation:
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cstrittmatter
parents:
diff changeset
411 #print "$$$Typhimurium"
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cstrittmatter
parents:
diff changeset
412 pass
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cstrittmatter
parents:
diff changeset
413 elif normal<mutation:
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cstrittmatter
parents:
diff changeset
414 predict_sero=predict_sero.strip()+"(O5-)"
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cstrittmatter
parents:
diff changeset
415 star="*"#
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cstrittmatter
parents:
diff changeset
416 star_line="Detected the deletion of O5-."
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cstrittmatter
parents:
diff changeset
417 #print "$$$Typhimurium_O5-"
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cstrittmatter
parents:
diff changeset
418 else:
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cstrittmatter
parents:
diff changeset
419 #print "$$$Typhimurium, even no 7 bases difference"
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cstrittmatter
parents:
diff changeset
420 pass
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cstrittmatter
parents:
diff changeset
421 return predict_form,predict_sero,star,star_line,claim
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cstrittmatter
parents:
diff changeset
422
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cstrittmatter
parents:
diff changeset
423 def main():
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cstrittmatter
parents:
diff changeset
424 database=sys.argv[1]#used to extract reads
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cstrittmatter
parents:
diff changeset
425 mapping_mode=sys.argv[2]#mem or sampe
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cstrittmatter
parents:
diff changeset
426 threads=sys.argv[3]
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cstrittmatter
parents:
diff changeset
427 for_fq=sys.argv[4]
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cstrittmatter
parents:
diff changeset
428 rev_fq=sys.argv[5]
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cstrittmatter
parents:
diff changeset
429 current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime())
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cstrittmatter
parents:
diff changeset
430 sam=for_fq+".sam"
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cstrittmatter
parents:
diff changeset
431 bam=for_fq+".bam"
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cstrittmatter
parents:
diff changeset
432 sorted_bam=for_fq+"_sorted.bam"
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cstrittmatter
parents:
diff changeset
433 mapped_fq1=for_fq+"_mapped.fq"
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cstrittmatter
parents:
diff changeset
434 mapped_fq2=rev_fq+"_mapped.fq"
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cstrittmatter
parents:
diff changeset
435 combined_fq=for_fq+"_combined.fq"
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cstrittmatter
parents:
diff changeset
436 for_sai=for_fq+".sai"
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cstrittmatter
parents:
diff changeset
437 rev_sai=rev_fq+".sai"
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cstrittmatter
parents:
diff changeset
438 print "building database..."
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cstrittmatter
parents:
diff changeset
439 #os.system("bwa index "+database+ " 2> /dev/null")
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cstrittmatter
parents:
diff changeset
440 os.system("bwa index "+database+ " 2>> data_log.txt ")
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cstrittmatter
parents:
diff changeset
441 print "mapping..."
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cstrittmatter
parents:
diff changeset
442 if mapping_mode=="mem":
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cstrittmatter
parents:
diff changeset
443 os.system("bwa mem -t "+threads+" "+database+" "+for_fq+" "+rev_fq+" > "+sam+ " 2>> data_log.txt")
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cstrittmatter
parents:
diff changeset
444 elif mapping_mode=="sam":
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cstrittmatter
parents:
diff changeset
445 os.system("bwa aln -t "+threads+" "+database+" "+for_fq+" > "+for_sai+ " 2>> data_log.txt")
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cstrittmatter
parents:
diff changeset
446 os.system("bwa aln -t "+threads+" "+database+" "+rev_fq+" > "+rev_sai+ " 2>> data_log.txt")
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cstrittmatter
parents:
diff changeset
447 os.system("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam+ " 2>> data_log.txt")
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cstrittmatter
parents:
diff changeset
448 os.system("samtools view -@ "+threads+" -F 4 -Sbh "+sam+" > "+bam)
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cstrittmatter
parents:
diff changeset
449 os.system("samtools view -@ "+threads+" -h -o "+sam+" "+bam)
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cstrittmatter
parents:
diff changeset
450 ### check the version of samtools then use differnt commands
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cstrittmatter
parents:
diff changeset
451 samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
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cstrittmatter
parents:
diff changeset
452 out, err = samtools_version.communicate()
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cstrittmatter
parents:
diff changeset
453 version = err.split("ersion:")[1].strip().split(" ")[0].strip()
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cstrittmatter
parents:
diff changeset
454 print "check samtools version:",version
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cstrittmatter
parents:
diff changeset
455 if LooseVersion(version)<=LooseVersion("1.2"):
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cstrittmatter
parents:
diff changeset
456 os.system("samtools sort -@ "+threads+" -n "+bam+" "+for_fq+"_sorted")
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cstrittmatter
parents:
diff changeset
457 else:
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cstrittmatter
parents:
diff changeset
458 os.system("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam)
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cstrittmatter
parents:
diff changeset
459 ### end of samtools version check and its analysis
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cstrittmatter
parents:
diff changeset
460 os.system("bamToFastq -i "+sorted_bam+" -fq "+combined_fq)
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cstrittmatter
parents:
diff changeset
461 os.system("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt")#2> /dev/null if want no output
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cstrittmatter
parents:
diff changeset
462 outdir=current_time+"_temp"
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cstrittmatter
parents:
diff changeset
463 print "assembling..."
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cstrittmatter
parents:
diff changeset
464 if int(threads)>4:
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cstrittmatter
parents:
diff changeset
465 t="4"
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cstrittmatter
parents:
diff changeset
466 else:
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cstrittmatter
parents:
diff changeset
467 t=threads
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cstrittmatter
parents:
diff changeset
468 os.system("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1")
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cstrittmatter
parents:
diff changeset
469 new_fasta=for_fq+"_"+database+"_"+mapping_mode+".fasta"
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cstrittmatter
parents:
diff changeset
470 os.system("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null")
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cstrittmatter
parents:
diff changeset
471 #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta
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cstrittmatter
parents:
diff changeset
472 os.system("rm -rf "+outdir+ " 2> /dev/null")
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cstrittmatter
parents:
diff changeset
473 ### begin blast
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cstrittmatter
parents:
diff changeset
474 print "blasting..."
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cstrittmatter
parents:
diff changeset
475 print "\n"
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cstrittmatter
parents:
diff changeset
476 xmlfile=for_fq+"-extracted_vs_"+database+"_"+mapping_mode+".xml"
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cstrittmatter
parents:
diff changeset
477 os.system('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1') #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015
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cstrittmatter
parents:
diff changeset
478 os.system("blastn -word_size 10 -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1")###1/27/2015
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cstrittmatter
parents:
diff changeset
479 Final_list=xml_parse_score_comparision_seqsero(xmlfile)
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cstrittmatter
parents:
diff changeset
480 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
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cstrittmatter
parents:
diff changeset
481 fliC_choice="-"
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cstrittmatter
parents:
diff changeset
482 fljB_choice="-"
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cstrittmatter
parents:
diff changeset
483 fliC_contig="NA"
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cstrittmatter
parents:
diff changeset
484 fljB_contig="NA"
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cstrittmatter
parents:
diff changeset
485 fliC_length=0 #can be changed to coverage in future
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cstrittmatter
parents:
diff changeset
486 fljB_length=0 #can be changed to coverage in future
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cstrittmatter
parents:
diff changeset
487 O_choice=""#no need to decide O contig for now, should be only one
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cstrittmatter
parents:
diff changeset
488 O_choice,O_nodes,special_gene_list,O_nodes_roles=decide_O_type_and_get_special_genes(Final_list)#decide the O antigen type and also return special-gene-list for further identification
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cstrittmatter
parents:
diff changeset
489 O_choice=O_choice.split("-")[-1].strip()
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cstrittmatter
parents:
diff changeset
490 H_contig_roles=decide_contig_roles_for_H_antigen(Final_list)#decide the H antigen contig is fliC or fljB
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cstrittmatter
parents:
diff changeset
491 log_file=open("SeqSero_hybrid_assembly_log.txt","a")
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cstrittmatter
parents:
diff changeset
492 print "O_contigs:"
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cstrittmatter
parents:
diff changeset
493 log_file.write("O_contigs:\n")
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cstrittmatter
parents:
diff changeset
494 for x in O_nodes_roles:
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cstrittmatter
parents:
diff changeset
495 if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker
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cstrittmatter
parents:
diff changeset
496 print x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%"
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cstrittmatter
parents:
diff changeset
497 log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+" "+"blast score: "+str(x[1])+"identity%:"+str(round(x[2]*100,2))+"%"+"\n")
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cstrittmatter
parents:
diff changeset
498 print "H_contigs:"
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cstrittmatter
parents:
diff changeset
499 log_file.write("H_contigs:\n")
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cstrittmatter
parents:
diff changeset
500 H_contig_stat=[]
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cstrittmatter
parents:
diff changeset
501 for i in range(len(H_contig_roles)):
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cstrittmatter
parents:
diff changeset
502 x=H_contig_roles[i]
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cstrittmatter
parents:
diff changeset
503 a=0
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cstrittmatter
parents:
diff changeset
504 for y in Final_list_passed:
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cstrittmatter
parents:
diff changeset
505 if x[1] in y[0] and y[0].startswith(x[0]):
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cstrittmatter
parents:
diff changeset
506 if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide
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cstrittmatter
parents:
diff changeset
507 for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it
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cstrittmatter
parents:
diff changeset
508 if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB
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cstrittmatter
parents:
diff changeset
509 print x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%"
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cstrittmatter
parents:
diff changeset
510 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+" "+"blast_score: "+str(y[1])+" identity%:"+str(round(y[2]*100,2))+"%"+"\n")
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cstrittmatter
parents:
diff changeset
511 H_contig_roles[i]="can't decide fliC or fljB, may be third phase"
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cstrittmatter
parents:
diff changeset
512 break
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cstrittmatter
parents:
diff changeset
513 else:
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cstrittmatter
parents:
diff changeset
514 print x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%"
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cstrittmatter
parents:
diff changeset
515 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+" "+"blast_score: "+str(y[1])+" identity%:"+str(round(y[2]*100,2))+"%"+"\n")
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cstrittmatter
parents:
diff changeset
516 break
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cstrittmatter
parents:
diff changeset
517 for x in H_contig_roles:
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cstrittmatter
parents:
diff changeset
518 #if multiple choices, temporately select the one with longest length for now, will revise in further change
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cstrittmatter
parents:
diff changeset
519 if "fliC" == x[0] and int(x[1].split("_")[3])>=fliC_length and x[1] not in O_nodes:#remember to avoid the effect of O-type contig, so should not in O_node list
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cstrittmatter
parents:
diff changeset
520 fliC_contig=x[1]
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cstrittmatter
parents:
diff changeset
521 fliC_length=int(x[1].split("_")[3])
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cstrittmatter
parents:
diff changeset
522 elif "fljB" == x[0] and int(x[1].split("_")[3])>=fljB_length and x[1] not in O_nodes:
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cstrittmatter
parents:
diff changeset
523 fljB_contig=x[1]
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cstrittmatter
parents:
diff changeset
524 fljB_length=int(x[1].split("_")[3])
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cstrittmatter
parents:
diff changeset
525 for x in Final_list_passed:
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cstrittmatter
parents:
diff changeset
526 if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0] :
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cstrittmatter
parents:
diff changeset
527 fliC_choice=x[0].split("_")[1]
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cstrittmatter
parents:
diff changeset
528 elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]:
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cstrittmatter
parents:
diff changeset
529 fljB_choice=x[0].split("_")[1]
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cstrittmatter
parents:
diff changeset
530 elif fliC_choice!="-" and fljB_choice!="-":
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cstrittmatter
parents:
diff changeset
531 break
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cstrittmatter
parents:
diff changeset
532 print "\n"
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cstrittmatter
parents:
diff changeset
533 print "SeqSero Input files:",for_fq,rev_fq
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cstrittmatter
parents:
diff changeset
534 print "Most possible O antigen:",O_choice
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cstrittmatter
parents:
diff changeset
535 print "Most possible H1 antigen:",fliC_choice
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cstrittmatter
parents:
diff changeset
536 print "Most possible H2 antigen:",fljB_choice
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cstrittmatter
parents:
diff changeset
537 #print Final_list
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cstrittmatter
parents:
diff changeset
538 ###output
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cstrittmatter
parents:
diff changeset
539 predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list)
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cstrittmatter
parents:
diff changeset
540 new_file=open("Seqsero_result.txt","w")
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cstrittmatter
parents:
diff changeset
541 new_file.write("Input files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+"O-"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
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cstrittmatter
parents:
diff changeset
542 new_file.close()
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cstrittmatter
parents:
diff changeset
543 os.system("cat Seqsero_result.txt")
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cstrittmatter
parents:
diff changeset
544
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cstrittmatter
parents:
diff changeset
545 if __name__ == '__main__':
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cstrittmatter
parents:
diff changeset
546 main()