Mercurial > repos > cpt > cpt_prophage_relatedness

annotate prophage_relatedness.py @ 0:7a23dda2e932 draft

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planemo upload commit 7ebbd0df0aea9e58c4df58b61d6da385ee0ebb49
author cpt
date Thu, 08 Aug 2024 03:09:32 +0000
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1 #!/usr/bin/env python
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2 import argparse
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3 from math import floor
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4 from Bio.Blast import NCBIXML
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5 import logging
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6
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7 logging.basicConfig(level=logging.DEBUG)
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8 log = logging.getLogger()
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9
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10
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11 def parseXML(blastxml, outFile): # Modified from intron_detection
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12 blast = []
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13 for iter_num, blast_record in enumerate(NCBIXML.parse(blastxml), 1):
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14 align_num = 0
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15 outFile.write("Query ID\tQuery Length\tTotal Number of Hits\n")
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16 outFile.write(
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17 "%s\t%d\t%d\n\n"
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18 % (
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19 blast_record.query_id,
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20 blast_record.query_length,
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21 len(blast_record.alignments),
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22 )
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23 )
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24
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25 for alignment in blast_record.alignments:
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26
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27 align_num += 1
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28 gi_nos = str(alignment.accession)
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29 blast_gene = []
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30 for hsp in alignment.hsps:
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31
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32 x = float(hsp.identities - 1) / ((hsp.query_end) - hsp.query_start)
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33 nice_name = blast_record.query
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34 if " " in nice_name:
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35 nice_name = nice_name[0 : nice_name.index(" ")]
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36 blast_gene.append(
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37 {
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38 "gi_nos": gi_nos,
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39 "sbjct_length": alignment.length,
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40 "query_length": blast_record.query_length,
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41 "sbjct_range": (hsp.sbjct_start, hsp.sbjct_end),
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42 "query_range": (hsp.query_start, hsp.query_end),
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43 "name": nice_name,
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44 "evalue": hsp.expect,
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45 "identity": hsp.identities,
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46 "identity_percent": x,
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47 "hit_num": align_num,
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48 "iter_num": iter_num,
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49 "match_id": alignment.title.partition(">")[0],
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50 "align_len": hsp.align_length,
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51 }
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52 )
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53 blast.append(blast_gene)
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54
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55 return blast
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56
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57
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58 def openTSV(blasttsv, outFile): # Modified from intron_detection
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59 blast = []
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60 activeAlign = ""
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61 numAlignments = 0
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62 qLen = 0
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63 for line in blasttsv:
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64 line = line.strip("\n")
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65 data = line.split("\t")
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66 for x in range(0, len(data)):
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67 data[x] = data[x].strip()
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68 qLen = data[22]
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69 if activeAlign == "":
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70 numAlignments += 1
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71 blast_gene = []
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72 hsp_num = 1
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73 elif activeAlign != data[1]:
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74 numAlignments += 1
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75 blast.append(blast_gene)
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76 blast_gene = []
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77 hsp_num = 1
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78 else:
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79 hsp_num += 1
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80 gi_nos = data[12]
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81 activeAlign = data[1]
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82 x = float(float(data[14]) - 1) / (float(data[7]) - float(data[6]))
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83 nice_name = data[1]
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84 if " " in nice_name:
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85 nice_name = nice_name[0 : nice_name.index(" ")]
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86 blast_gene.append(
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87 {
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88 "gi_nos": gi_nos,
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89 "sbjct_length": int(data[23]),
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90 "query_length": int(data[22]),
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91 "sbjct_range": (int(data[8]), int(data[9])),
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92 "query_range": (int(data[6]), int(data[7])),
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93 "name": nice_name,
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94 "evalue": float(data[10]),
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95 "identity": int(data[14]),
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96 "identity_percent": x,
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97 "hit_num": numAlignments,
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98 "iter_num": hsp_num,
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99 "match_id": data[24].partition(">")[0],
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100 "align_len": int(data[3]),
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101 }
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102 )
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103
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104 blast.append(blast_gene)
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105 outFile.write("Query ID\tQuery Length\tTotal Number of Hits\n")
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106 outFile.write("%s\t%d\t%d\n\n" % (data[0], int(data[22]), numAlignments))
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107
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108 return blast
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109
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110
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111 def test_true(feature, **kwargs):
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112 return True
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113
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114
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115 def superSets(inSets):
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116 inSets.sort(key=len, reverse=True)
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117 nextInd = 0
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118 res = []
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119 for i in range(0, len(inSets)):
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120 if i == 0:
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121 res.append(inSets[i])
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122 continue
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123 for par in res:
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124 complete = True
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125 for x in inSets[i]:
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126 if not (x in par):
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parents:
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127 complete = False
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parents:
diff changeset
128 if complete:
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parents:
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129 break # Subset of at least one member
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cpt
parents:
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130 if not complete:
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131 res.append(inSets[i])
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132 return res
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parents:
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133
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cpt
parents:
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134
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parents:
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135 def disjointSets(inSets):
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parents:
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136 inSets.sort(key=lambda x: x[0]["sbjct_range"][0])
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137 res = [inSets[0]]
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parents:
diff changeset
138 for i in range(1, len(inSets)):
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139 disjoint = True
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parents:
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140 for elem in inSets[i]:
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cpt
parents:
diff changeset
141 for cand in res:
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cpt
parents:
diff changeset
142 if elem in cand:
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parents:
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143 disjoint = False
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parents:
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144 break
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cpt
parents:
diff changeset
145 if not disjoint:
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cpt
parents:
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146 break
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parents:
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147 if disjoint:
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148 res.append(inSets[i])
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cpt
parents:
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149 return res
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150
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parents:
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151
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152 def compPhage(inRec, outFile, padding=1.2, cutoff=0.3, numReturn=20, isTSV=False):
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153
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154 if isTSV:
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155 inRec = openTSV(inRec, outFile)
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156 else:
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157 inRec = parseXML(inRec, outFile)
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158 res = []
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parents:
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159 for group in inRec:
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160 window = floor(padding * float(group[0]["query_length"]))
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161 group = sorted(group, key=lambda x: x["sbjct_range"][0])
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parents:
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162 hspGroups = []
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parents:
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163 lastInd = len(res)
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parents:
diff changeset
164
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parents:
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165 for x in range(0, len(group)):
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parents:
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166 hspGroups.append([group[x]])
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parents:
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167 startBound = group[x]["sbjct_range"][0]
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parents:
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168 endBound = startBound + window
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parents:
diff changeset
169 for hsp in group[x + 1 :]:
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cpt
parents:
diff changeset
170 if (
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cpt
parents:
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171 hsp["sbjct_range"][0] >= startBound
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172 and hsp["sbjct_range"][1] <= endBound
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parents:
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173 ):
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parents:
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174 hspGroups[-1].append(hsp)
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cpt
parents:
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175
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176 for x in disjointSets(superSets(hspGroups)):
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parents:
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177 res.append(x)
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parents:
diff changeset
178
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parents:
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179 maxID = 0.0
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parents:
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180 for x in res[lastInd:]:
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cpt
parents:
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181 sumID = 0.0
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parents:
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182 totAlign = 0
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cpt
parents:
diff changeset
183 for y in x:
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parents:
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184 totAlign += y["align_len"]
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parents:
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185 sumID += float(y["identity"])
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parents:
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186 x.append(totAlign)
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parents:
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187 x.append(sumID / float(x[0]["query_length"]))
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188 maxID = max(maxID, x[-1])
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cpt
parents:
diff changeset
189
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parents:
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190 res = sorted(res, key=lambda x: x[-1], reverse=True)
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cpt
parents:
diff changeset
191
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parents:
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192 outList = []
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parents:
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193 outNum = 0
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cpt
parents:
diff changeset
194 for x in res:
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parents:
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195 if outNum == numReturn or x[-1] < cutoff:
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cpt
parents:
diff changeset
196 break
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cpt
parents:
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197 outNum += 1
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parents:
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198 outList.append(x)
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cpt
parents:
diff changeset
199
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cpt
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200 # Original request was that low scoring clusters would make it to the final results IF
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cpt
parents:
diff changeset
201 # they were part of an Accession cluster that did have at least one high scoring member.
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cpt
parents:
diff changeset
202
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cpt
parents:
diff changeset
203 outFile.write(
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parents:
diff changeset
204 "Accession Number\tCluster Start Location\tEnd Location\tSubject Cluster Length\t# HSPs in Cluster\tTotal Aligned Length\t% of Query Aligned\tOverall % Query Identity\tOverall % Subject Identity\tComplete Accession Info\n"
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cpt
parents:
diff changeset
205 )
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cpt
parents:
diff changeset
206 for x in outList:
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cpt
parents:
diff changeset
207 minStart = min(x[0]["sbjct_range"][0], x[0]["sbjct_range"][1])
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cpt
parents:
diff changeset
208 maxEnd = max(x[0]["sbjct_range"][0], x[0]["sbjct_range"][1])
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cpt
parents:
diff changeset
209 if "|gb|" in x[0]["match_id"]:
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cpt
parents:
diff changeset
210 startSlice = x[0]["match_id"].index("gb|") + 3
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cpt
parents:
diff changeset
211 endSlice = (x[0]["match_id"][startSlice:]).index("|")
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cpt
parents:
diff changeset
212 accOut = x[0]["match_id"][startSlice : startSlice + endSlice]
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cpt
parents:
diff changeset
213 else:
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cpt
parents:
diff changeset
214 accOut = x[0]["gi_nos"]
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cpt
parents:
diff changeset
215 for y in x[0:-2]:
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cpt
parents:
diff changeset
216 # ("\t%.3f\t" % (x[-1]))
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cpt
parents:
diff changeset
217 minStart = min(minStart, y["sbjct_range"][0])
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cpt
parents:
diff changeset
218 maxEnd = max(maxEnd, y["sbjct_range"][1])
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cpt
parents:
diff changeset
219 outFile.write(
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cpt
parents:
diff changeset
220 accOut
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cpt
parents:
diff changeset
221 + "\t"
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cpt
parents:
diff changeset
222 + str(minStart)
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cpt
parents:
diff changeset
223 + "\t"
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cpt
parents:
diff changeset
224 + str(maxEnd)
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cpt
parents:
diff changeset
225 + "\t"
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cpt
parents:
diff changeset
226 + str(maxEnd - minStart + 1)
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cpt
parents:
diff changeset
227 + "\t"
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cpt
parents:
diff changeset
228 + str(len(x) - 1)
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cpt
parents:
diff changeset
229 + "\t"
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cpt
parents:
diff changeset
230 + str(x[-2])
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cpt
parents:
diff changeset
231 + ("\t%.3f" % (float(x[-2]) / float(x[0]["query_length"]) * 100.00))
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cpt
parents:
diff changeset
232 + ("\t%.3f" % (x[-1] * 100.00))
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cpt
parents:
diff changeset
233 + ("\t%.3f" % (float(x[-2]) / float(maxEnd - minStart + 1) * 100.00))
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cpt
parents:
diff changeset
234 + "\t"
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cpt
parents:
diff changeset
235 + x[0]["match_id"]
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cpt
parents:
diff changeset
236 + "\n"
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cpt
parents:
diff changeset
237 )
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cpt
parents:
diff changeset
238
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cpt
parents:
diff changeset
239 # accession start end number
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cpt
parents:
diff changeset
240
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cpt
parents:
diff changeset
241
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cpt
parents:
diff changeset
242 if __name__ == "__main__":
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cpt
parents:
diff changeset
243 parser = argparse.ArgumentParser(description="Intron detection")
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cpt
parents:
diff changeset
244 parser.add_argument(
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cpt
parents:
diff changeset
245 "inRec", type=argparse.FileType("r"), help="blast XML protein results"
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cpt
parents:
diff changeset
246 )
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cpt
parents:
diff changeset
247 parser.add_argument(
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cpt
parents:
diff changeset
248 "--outFile",
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cpt
parents:
diff changeset
249 type=argparse.FileType("w"),
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cpt
parents:
diff changeset
250 help="Output Error Log",
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cpt
parents:
diff changeset
251 default="./compPro.tsv",
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cpt
parents:
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252 )
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253 parser.add_argument(
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254 "--padding",
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255 help="Gap minimum (Default -1, set to a negative number to allow overlap)",
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256 default=1.2,
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257 type=float,
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258 )
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259 parser.add_argument(
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260 "--cutoff",
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261 help="Gap minimum (Default -1, set to a negative number to allow overlap)",
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262 default=0.3,
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263 type=float,
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264 )
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265 parser.add_argument(
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266 "--numReturn",
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267 help="Gap maximum in genome (Default 10000)",
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268 default=20,
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269 type=int,
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270 )
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271 parser.add_argument(
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272 "--isTSV",
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273 help="Opening Blast TSV result",
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274 action="store_true",
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275 )
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276 args = parser.parse_args()
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277
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278 compPhage(**vars(args))