Mercurial > repos > davidvanzessen > shm_csr
annotate shm_csr.py @ 99:5b79485234e1 draft default tip
planemo upload commit 0d652311f9c4ccc26b27eebc44a3ae91a72e57b0
| author | rhpvorderman |
|---|---|
| date | Mon, 03 Feb 2025 13:37:26 +0000 |
| parents | 385dea3c6cb5 |
| children |
| rev | line source |
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| 81 | 1 import argparse |
| 2 import logging | |
| 3 import sys | |
| 4 import os | |
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5 import traceback |
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6 import typing |
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7 from typing import Optional |
| 81 | 8 |
| 9 from collections import defaultdict | |
| 10 | |
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11 REGION_FILTERS = ("leader", "FR1", "CDR1", "FR2", "CDR2", "None") |
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12 |
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13 |
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14 def int_or_zero(value: typing.Any): |
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15 try: |
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16 return int(value) |
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17 except ValueError: |
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18 return 0 |
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19 |
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20 class Mutation(typing.NamedTuple): |
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21 """Represent a mutation type as a tuple""" |
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22 frm: str # 'from' is a reserved python keyword. |
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23 where: int |
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24 to: str |
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25 frmAA: Optional[str] = None |
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26 whereAA: Optional[int] = None |
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27 toAA: Optional[str] = None |
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28 thing: Optional[str] = None # '(---)' or '(+-+)' etc. No idea |
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29 |
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30 @classmethod |
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31 def from_string(cls, string: str): |
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32 # Complete mutation example: a88>g,I30>V(+ - +) |
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33 # Only nucleotide example: g303>t |
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34 # Including codon change: |
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35 # t169>g,Y57>D(- - -); Y57 tat 169-171 [ta 169-170]>D gac |
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36 # Including codon change (synonumous mutation): |
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37 # c114>t, Y38; Y38 tac 112-114 [tact 112-115]>Y tat |
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38 if ',' in string: |
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39 nucleotide_change, aa_change = string.split(',', maxsplit=1) # type: str, Optional[str] |
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40 else: |
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41 nucleotide_change = string |
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42 aa_change = None |
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43 frm_part, to = nucleotide_change.split('>', maxsplit=1) |
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44 frm = frm_part[0] |
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45 where = int(frm_part[1:]) |
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46 |
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47 if aa_change is None: |
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48 return cls(frm, where, to) |
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49 |
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50 aa_change = aa_change.strip() |
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51 # The part after semicolon indicates the codon change. This part may |
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52 # not be present. |
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53 semi_colon_index = aa_change.find(";") |
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54 if semi_colon_index == -1: |
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55 codon_change = "" |
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56 else: |
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57 codon_change = aa_change[semi_colon_index:] |
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58 aa_change = aa_change[:semi_colon_index] |
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59 change_operator_index = aa_change.find(">") |
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60 if change_operator_index == -1: |
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61 # Synonymous change |
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62 frmAA_part = aa_change |
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63 toAA_part = "" |
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64 else: |
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65 frmAA_part, toAA_part = aa_change.split('>', maxsplit=1) # type: str, str |
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66 frmAA = frmAA_part[0] |
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67 whereAA = int(frmAA_part[1:]) |
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68 if toAA_part: |
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69 brace_start = toAA_part.index('(') |
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70 toAA = toAA_part[:brace_start] |
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71 thing = toAA_part[brace_start:] + codon_change |
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72 else: |
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73 # Synonymous mutation |
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74 toAA = frmAA |
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75 thing = codon_change |
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76 return cls(frm, where, to, frmAA, whereAA, toAA, thing) |
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77 |
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78 |
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79 class Hotspot(typing.NamedTuple): |
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80 start: int |
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81 end: int |
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82 region: str |
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83 |
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84 @classmethod |
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85 def from_string(cls, string): |
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86 # Example: aa,40-41(FR1) |
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87 sequence, rest = string.split(',') # type: str, str |
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88 brace_pos = rest.index('(') |
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89 numbers = rest[:brace_pos] |
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90 start, end = numbers.split('-') |
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91 region = rest[brace_pos + 1:-1] # Remove the braces |
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92 return cls(int(start), int(end), region) |
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93 |
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94 |
| 81 | 95 def main(): |
| 96 parser = argparse.ArgumentParser() | |
| 97 parser.add_argument("--input", help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation") | |
| 98 parser.add_argument("--genes", help="The genes available in the 'best_match' column") | |
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99 parser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=REGION_FILTERS) |
| 81 | 100 parser.add_argument("--output", help="Output file") |
| 101 | |
| 102 args = parser.parse_args() | |
| 103 | |
| 104 infile = args.input | |
| 105 genes = str(args.genes).split(",") | |
| 106 empty_region_filter = args.empty_region_filter | |
| 107 outfile = args.output | |
| 108 | |
| 109 genedic = dict() | |
| 110 | |
| 111 mutationdic = dict() | |
| 112 NAMatchResult = (None, None, None, None, None, None, '') | |
| 113 linecount = 0 | |
| 114 | |
| 115 IDIndex = 0 | |
| 116 best_matchIndex = 0 | |
| 117 fr1Index = 0 | |
| 118 cdr1Index = 0 | |
| 119 fr2Index = 0 | |
| 120 cdr2Index = 0 | |
| 121 fr3Index = 0 | |
| 122 first = True | |
| 123 IDlist = [] | |
| 124 mutationList = [] | |
| 125 mutationListByID = {} | |
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126 cdr1AALengthDic = {} |
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127 cdr2AALengthDic = {} |
| 81 | 128 |
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129 LengthDic = {} |
| 81 | 130 |
| 131 cdr1LengthIndex = 0 | |
| 132 cdr2LengthIndex = 0 | |
| 133 | |
| 134 tandem_sum_by_class = defaultdict(int) | |
| 135 expected_tandem_sum_by_class = defaultdict(float) | |
| 136 | |
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137 with open(infile, 'r') as i: |
| 81 | 138 for line in i: |
| 139 if first: | |
| 140 linesplt = line.split("\t") | |
| 141 IDIndex = linesplt.index("Sequence.ID") | |
| 142 best_matchIndex = linesplt.index("best_match") | |
| 143 fr1Index = linesplt.index("FR1.IMGT") | |
| 144 cdr1Index = linesplt.index("CDR1.IMGT") | |
| 145 fr2Index = linesplt.index("FR2.IMGT") | |
| 146 cdr2Index = linesplt.index("CDR2.IMGT") | |
| 147 fr3Index = linesplt.index("FR3.IMGT") | |
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148 fr1LengthIndex = linesplt.index("FR1.IMGT.Nb.of.nucleotides") |
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149 fr2LengthIndex = linesplt.index("FR2.IMGT.Nb.of.nucleotides") |
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150 fr3LengthIndex = linesplt.index("FR3.IMGT.Nb.of.nucleotides") |
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151 cdr1LengthIndex = linesplt.index("CDR1.IMGT.Nb.of.nucleotides") |
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152 cdr2LengthIndex = linesplt.index("CDR2.IMGT.Nb.of.nucleotides") |
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153 cdr1AALengthIndex = linesplt.index("CDR1.IMGT.length") |
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154 cdr2AALengthIndex = linesplt.index("CDR2.IMGT.length") |
| 81 | 155 first = False |
| 156 continue | |
| 157 linecount += 1 | |
| 158 linesplt = line.split("\t") | |
| 159 ID = linesplt[IDIndex] | |
| 160 genedic[ID] = linesplt[best_matchIndex] | |
| 161 | |
| 162 mutationdic[ID + "_FR1"] = [] | |
| 163 if len(linesplt[fr1Index]) > 5 and empty_region_filter == "leader": | |
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164 mutationdic[ID + "_FR1"] = [Mutation.from_string(x) for x in linesplt[fr1Index].split("|") if x] |
| 81 | 165 |
| 166 mutationdic[ID + "_CDR1"] = [] | |
| 167 if len(linesplt[cdr1Index]) > 5 and empty_region_filter in ["leader", "FR1"]: | |
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168 mutationdic[ID + "_CDR1"] = [Mutation.from_string(x) for x in linesplt[cdr1Index].split("|") if x] |
| 81 | 169 |
| 170 mutationdic[ID + "_FR2"] = [] | |
| 171 if len(linesplt[fr2Index]) > 5 and empty_region_filter in ["leader", "FR1", "CDR1"]: | |
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172 mutationdic[ID + "_FR2"] = [Mutation.from_string(x) for x in linesplt[fr2Index].split("|") if x] |
| 81 | 173 |
| 174 mutationdic[ID + "_CDR2"] = [] | |
| 175 if len(linesplt[cdr2Index]) > 5: | |
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176 mutationdic[ID + "_CDR2"] = [Mutation.from_string(x) for x in linesplt[cdr2Index].split("|") if x] |
| 81 | 177 |
| 178 mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] | |
| 179 | |
| 180 mutationdic[ID + "_FR3"] = [] | |
| 181 if len(linesplt[fr3Index]) > 5: | |
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182 mutationdic[ID + "_FR3"] = [Mutation.from_string(x) for x in linesplt[fr3Index].split("|") if x] |
| 81 | 183 |
| 184 mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] | |
| 185 mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] | |
| 186 | |
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187 fr1Length = int_or_zero(linesplt[fr1LengthIndex]) |
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188 fr2Length = int_or_zero(linesplt[fr2LengthIndex]) |
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189 fr3Length = int_or_zero(linesplt[fr3LengthIndex]) |
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190 cdr1Length = int_or_zero(linesplt[cdr1LengthIndex]) |
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191 cdr2Length = int_or_zero(linesplt[cdr2LengthIndex]) |
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192 LengthDic[ID] = (fr1Length, cdr1Length, fr2Length, cdr2Length, fr3Length) |
| 81 | 193 |
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194 cdr1AALengthDic[ID] = int_or_zero(linesplt[cdr1AALengthIndex]) |
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195 cdr2AALengthDic[ID] = int_or_zero(linesplt[cdr2AALengthIndex]) |
| 81 | 196 |
| 197 IDlist += [ID] | |
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198 print("len(mutationdic) =", len(mutationdic)) |
| 81 | 199 |
| 200 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "mutationdict.txt"), 'w') as out_handle: | |
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201 for ID, lst in mutationdic.items(): |
| 81 | 202 for mut in lst: |
| 203 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in mut]))) | |
| 204 | |
| 205 #tandem mutation stuff | |
| 206 tandem_frequency = defaultdict(int) | |
| 207 mutation_frequency = defaultdict(int) | |
| 208 | |
| 209 mutations_by_id_dic = {} | |
| 210 first = True | |
| 211 mutation_by_id_file = os.path.join(os.path.dirname(outfile), "mutation_by_id.txt") | |
| 212 with open(mutation_by_id_file, 'r') as mutation_by_id: | |
| 213 for l in mutation_by_id: | |
| 214 if first: | |
| 215 first = False | |
| 216 continue | |
| 217 splt = l.split("\t") | |
| 218 mutations_by_id_dic[splt[0]] = int(splt[1]) | |
| 219 | |
| 220 tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt") | |
| 221 with open(tandem_file, 'w') as o: | |
| 222 highest_tandem_length = 0 | |
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223 # LengthDic stores length as a tuple |
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224 # (fr1Length, cdr1Length, fr2Length, cdr2Length, fr3Length) |
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225 # To get the total length, we can sum(region_lengths) |
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226 # To get the total length for leader: |
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227 # sum(region_lengths[0:]) (Equivalent to everything) |
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228 # sum(region_lengths[1:]) Gets everything except FR1 etc. |
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229 # We determine the position to start summing below. |
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230 # This returns 0 for leader, 1 for FR1 etc. |
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231 length_start_pos = REGION_FILTERS.index(empty_region_filter) |
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232 if empty_region_filter == "None": |
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233 length_start_pos = 0 |
| 81 | 234 |
| 235 o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n") | |
| 236 for ID in IDlist: | |
| 237 mutations = mutationListByID[ID] | |
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238 region_length = sum(LengthDic[ID][length_start_pos:]) |
| 81 | 239 if len(mutations) == 0: |
| 240 continue | |
| 241 last_mut = max(mutations, key=lambda x: int(x[1])) | |
| 242 | |
| 243 last_mut_pos = int(last_mut[1]) | |
| 244 | |
| 245 mut_positions = [False] * (last_mut_pos + 1) | |
| 246 | |
| 247 for mutation in mutations: | |
| 248 frm, where, to, frmAA, whereAA, toAA, thing = mutation | |
| 249 where = int(where) | |
| 250 mut_positions[where] = True | |
| 251 | |
| 252 tandem_muts = [] | |
| 253 tandem_start = -1 | |
| 254 tandem_length = 0 | |
| 255 for i in range(len(mut_positions)): | |
| 256 if mut_positions[i]: | |
| 257 if tandem_start == -1: | |
| 258 tandem_start = i | |
| 259 tandem_length += 1 | |
| 260 #print "".join(["1" if x else "0" for x in mut_positions[:i+1]]) | |
| 261 else: | |
| 262 if tandem_length > 1: | |
| 263 tandem_muts.append((tandem_start, tandem_length)) | |
| 264 #print "{0}{1} {2}:{3}".format(" " * (i - tandem_length), "^" * tandem_length, tandem_start, tandem_length) | |
| 265 tandem_start = -1 | |
| 266 tandem_length = 0 | |
| 267 if tandem_length > 1: # if the sequence ends with a tandem mutation | |
| 268 tandem_muts.append((tandem_start, tandem_length)) | |
| 269 | |
| 270 if len(tandem_muts) > 0: | |
| 271 if highest_tandem_length < len(tandem_muts): | |
| 272 highest_tandem_length = len(tandem_muts) | |
| 273 | |
| 274 longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0) | |
| 275 num_mutations = mutations_by_id_dic[ID] # len(mutations) | |
| 276 f_num_mutations = float(num_mutations) | |
| 277 num_tandem_muts = len(tandem_muts) | |
| 278 expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length) | |
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279 # String format and round disagree slightly (see 3.605). |
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280 # So round before formatting. |
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281 o.write(f"{ID}\t{num_mutations}\t{num_tandem_muts}\t{region_length}\t" |
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282 f"{round(expected_tandem_muts, 2):.2f}\t" |
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283 f"{longest_tandem[1]}\t{tandem_muts}\n") |
| 81 | 284 gene = genedic[ID] |
| 285 if gene.find("unmatched") == -1: | |
| 286 tandem_sum_by_class[gene] += num_tandem_muts | |
| 287 expected_tandem_sum_by_class[gene] += expected_tandem_muts | |
| 288 | |
| 289 tandem_sum_by_class["all"] += num_tandem_muts | |
| 290 expected_tandem_sum_by_class["all"] += expected_tandem_muts | |
| 291 | |
| 292 gene = gene[:3] | |
| 293 if gene in ["IGA", "IGG"]: | |
| 294 tandem_sum_by_class[gene] += num_tandem_muts | |
| 295 expected_tandem_sum_by_class[gene] += expected_tandem_muts | |
| 296 else: | |
| 297 tandem_sum_by_class["unmatched"] += num_tandem_muts | |
| 298 expected_tandem_sum_by_class["unmatched"] += expected_tandem_muts | |
| 299 | |
| 300 | |
| 301 for tandem_mut in tandem_muts: | |
| 302 tandem_frequency[str(tandem_mut[1])] += 1 | |
| 303 #print "\t".join([ID, str(len(tandem_muts)), str(longest_tandem[1]) , str(tandem_muts)]) | |
| 304 | |
| 305 tandem_freq_file = os.path.join(os.path.dirname(outfile), "tandem_frequency.txt") | |
| 306 with open(tandem_freq_file, 'w') as o: | |
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307 for frq in sorted([int(x) for x in list(tandem_frequency.keys())]): |
| 81 | 308 o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)])) |
| 309 | |
| 310 tandem_row = [] | |
| 311 genes_extra = list(genes) | |
| 312 genes_extra.append("all") | |
| 313 for x, y, in zip([tandem_sum_by_class[x] for x in genes_extra], [expected_tandem_sum_by_class[x] for x in genes_extra]): | |
| 314 if y != 0: | |
| 315 tandem_row += [x, round(y, 2), round(x / y, 2)] | |
| 316 else: | |
| 317 tandem_row += [x, round(y, 2), 0] | |
| 318 | |
| 319 tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt") | |
| 320 with open(tandem_freq_file, 'w') as o: | |
| 321 o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row]))) | |
| 322 | |
| 323 #print mutationList, linecount | |
| 324 | |
| 325 AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] and i[5] != ";" else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent | |
| 326 if AALength < 60: | |
| 327 AALength = 64 | |
| 328 | |
| 329 AA_mutation = [0] * AALength | |
| 330 AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]} | |
| 331 AA_mutation_empty = AA_mutation[:] | |
| 332 | |
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333 print("AALength:", AALength) |
| 81 | 334 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt" |
| 335 with open(aa_mutations_by_id_file, 'w') as o: | |
| 336 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n") | |
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337 for ID in list(mutationListByID.keys()): |
| 81 | 338 AA_mutation_for_ID = AA_mutation_empty[:] |
| 339 for mutation in mutationListByID[ID]: | |
| 340 if mutation[4] and mutation[5] != ";": | |
| 341 AA_mutation_position = int(mutation[4]) | |
| 342 try: | |
| 343 AA_mutation[AA_mutation_position] += 1 | |
| 344 AA_mutation_for_ID[AA_mutation_position] += 1 | |
| 345 except Exception as e: | |
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346 print(e) |
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347 print(mutation) |
| 81 | 348 sys.exit() |
| 349 clss = genedic[ID][:3] | |
| 350 AA_mutation_dic[clss][AA_mutation_position] += 1 | |
| 351 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n") | |
| 352 | |
| 353 | |
| 354 | |
| 355 #absent AA stuff | |
| 356 absentAACDR1Dic = defaultdict(list) | |
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357 absentAACDR1Dic[5] = list(range(29,36)) |
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358 absentAACDR1Dic[6] = list(range(29,35)) |
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359 absentAACDR1Dic[7] = list(range(30,35)) |
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360 absentAACDR1Dic[8] = list(range(30,34)) |
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361 absentAACDR1Dic[9] = list(range(31,34)) |
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362 absentAACDR1Dic[10] = list(range(31,33)) |
| 81 | 363 absentAACDR1Dic[11] = [32] |
| 364 | |
| 365 absentAACDR2Dic = defaultdict(list) | |
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366 absentAACDR2Dic[0] = list(range(55,65)) |
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367 absentAACDR2Dic[1] = list(range(56,65)) |
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368 absentAACDR2Dic[2] = list(range(56,64)) |
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369 absentAACDR2Dic[3] = list(range(57,64)) |
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370 absentAACDR2Dic[4] = list(range(57,63)) |
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371 absentAACDR2Dic[5] = list(range(58,63)) |
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372 absentAACDR2Dic[6] = list(range(58,62)) |
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373 absentAACDR2Dic[7] = list(range(59,62)) |
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374 absentAACDR2Dic[8] = list(range(59,61)) |
| 81 | 375 absentAACDR2Dic[9] = [60] |
| 376 | |
| 377 absentAA = [len(IDlist)] * (AALength-1) | |
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378 for k, cdr1Length in cdr1AALengthDic.items(): |
| 81 | 379 for c in absentAACDR1Dic[cdr1Length]: |
| 380 absentAA[c] -= 1 | |
| 381 | |
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382 for k, cdr2Length in cdr2AALengthDic.items(): |
| 81 | 383 for c in absentAACDR2Dic[cdr2Length]: |
| 384 absentAA[c] -= 1 | |
| 385 | |
| 386 | |
| 387 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt" | |
| 388 with open(aa_mutations_by_id_file, 'w') as o: | |
| 389 o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n") | |
| 390 for ID in IDlist: | |
| 391 absentAAbyID = [1] * (AALength-1) | |
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392 cdr1Length = cdr1AALengthDic[ID] |
| 81 | 393 for c in absentAACDR1Dic[cdr1Length]: |
| 394 absentAAbyID[c] -= 1 | |
| 395 | |
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396 cdr2Length = cdr2AALengthDic[ID] |
| 81 | 397 for c in absentAACDR2Dic[cdr2Length]: |
| 398 absentAAbyID[c] -= 1 | |
| 399 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n") | |
| 400 | |
| 401 if linecount == 0: | |
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402 print("No data, exiting") |
| 81 | 403 with open(outfile, 'w') as o: |
| 404 o.write("RGYW (%)," + ("0,0,0\n" * len(genes))) | |
| 405 o.write("WRCY (%)," + ("0,0,0\n" * len(genes))) | |
| 406 o.write("WA (%)," + ("0,0,0\n" * len(genes))) | |
| 407 o.write("TW (%)," + ("0,0,0\n" * len(genes))) | |
| 408 sys.exit() | |
| 409 | |
| 410 RGYWCount = {} | |
| 411 WRCYCount = {} | |
| 412 WACount = {} | |
| 413 TWCount = {} | |
| 414 | |
| 415 #IDIndex = 0 | |
| 416 ataIndex = 0 | |
| 417 tatIndex = 0 | |
| 418 aggctatIndex = 0 | |
| 419 atagcctIndex = 0 | |
| 420 first = True | |
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421 with open(infile, 'r') as i: |
| 81 | 422 for line in i: |
| 423 if first: | |
| 424 linesplt = line.split("\t") | |
| 425 ataIndex = linesplt.index("X.a.t.a") | |
| 426 tatIndex = linesplt.index("t.a.t.") | |
| 427 aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.") | |
| 428 atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.") | |
| 429 first = False | |
| 430 continue | |
| 431 linesplt = line.split("\t") | |
| 432 gene = linesplt[best_matchIndex] | |
| 433 ID = linesplt[IDIndex] | |
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434 RGYW = [Hotspot.from_string(x) for x in linesplt[aggctatIndex].split("|") if x] |
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435 WRCY = [Hotspot.from_string(x) for x in linesplt[atagcctIndex].split("|") if x] |
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436 WA = [Hotspot.from_string(x) for x in linesplt[ataIndex].split("|") if x] |
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437 TW = [Hotspot.from_string(x) for x in linesplt[tatIndex].split("|") if x] |
| 81 | 438 RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0 |
| 439 | |
| 440 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "RGYW.txt"), 'a') as out_handle: | |
| 441 for hotspot in RGYW: | |
| 442 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in hotspot]))) | |
| 443 | |
| 444 mutationList = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] | |
| 445 for mutation in mutationList: | |
| 446 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation | |
| 447 mutation_in_RGYW = any(((start <= int(where) <= end) for (start, end, region) in RGYW)) | |
| 448 mutation_in_WRCY = any(((start <= int(where) <= end) for (start, end, region) in WRCY)) | |
| 449 mutation_in_WA = any(((start <= int(where) <= end) for (start, end, region) in WA)) | |
| 450 mutation_in_TW = any(((start <= int(where) <= end) for (start, end, region) in TW)) | |
| 451 | |
| 452 in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW]) | |
| 453 | |
| 454 if in_how_many_motifs > 0: | |
| 455 RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs | |
| 456 WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs | |
| 457 WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs | |
| 458 TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs | |
| 459 | |
| 460 mutations_in_motifs_file = os.path.join(os.path.dirname(os.path.abspath(infile)), "mutation_in_motifs.txt") | |
| 461 if not os.path.exists(mutation_by_id_file): | |
| 462 with open(mutations_in_motifs_file, 'w') as out_handle: | |
| 463 out_handle.write("{0}\n".format("\t".join([ | |
| 464 "Sequence.ID", | |
| 465 "mutation_position", | |
| 466 "region", | |
| 467 "from_nt", | |
| 468 "to_nt", | |
| 469 "mutation_position_AA", | |
| 470 "from_AA", | |
| 471 "to_AA", | |
| 472 "motif", | |
| 473 "motif_start_nt", | |
| 474 "motif_end_nt", | |
| 475 "rest" | |
| 476 ]))) | |
| 477 | |
| 478 with open(mutations_in_motifs_file, 'a') as out_handle: | |
| 479 motif_dic = {"RGYW": RGYW, "WRCY": WRCY, "WA": WA, "TW": TW} | |
| 480 for mutation in mutationList: | |
| 481 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation | |
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482 for motif in list(motif_dic.keys()): |
| 81 | 483 |
| 484 for start, end, region in motif_dic[motif]: | |
| 485 if start <= int(where) <= end: | |
| 486 out_handle.write("{0}\n".format( | |
| 487 "\t".join([ | |
| 488 ID, | |
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489 str(where), |
| 81 | 490 region, |
| 491 frm, | |
| 492 to, | |
| 493 str(AAwhere), | |
| 494 str(AAfrm), | |
| 495 str(AAto), | |
| 496 motif, | |
| 497 str(start), | |
| 498 str(end), | |
| 499 str(junk) | |
| 500 ]) | |
| 501 )) | |
| 502 | |
| 503 | |
| 504 | |
| 505 def mean(lst): | |
| 506 return (float(sum(lst)) / len(lst)) if len(lst) > 0 else 0.0 | |
| 507 | |
| 508 | |
| 509 def median(lst): | |
| 510 lst = sorted(lst) | |
| 511 l = len(lst) | |
| 512 if l == 0: | |
| 513 return 0 | |
| 514 if l == 1: | |
| 515 return lst[0] | |
| 516 | |
| 517 l = int(l / 2) | |
| 518 | |
| 519 if len(lst) % 2 == 0: | |
| 520 return float(lst[l] + lst[(l - 1)]) / 2.0 | |
| 521 else: | |
| 522 return lst[l] | |
| 523 | |
| 524 funcs = {"mean": mean, "median": median, "sum": sum} | |
| 525 | |
| 526 directory = outfile[:outfile.rfind("/") + 1] | |
| 527 value = 0 | |
| 528 valuedic = dict() | |
| 529 | |
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530 for fname in list(funcs.keys()): |
| 81 | 531 for gene in genes: |
| 532 with open(directory + gene + "_" + fname + "_value.txt", 'r') as v: | |
| 533 valuedic[gene + "_" + fname] = float(v.readlines()[0].rstrip()) | |
| 534 with open(directory + "all_" + fname + "_value.txt", 'r') as v: | |
| 535 valuedic["total_" + fname] = float(v.readlines()[0].rstrip()) | |
| 536 | |
| 537 | |
| 538 def get_xyz(lst, gene, f, fname): | |
| 539 x = round(round(f(lst), 1)) | |
| 540 y = valuedic[gene + "_" + fname] | |
| 541 z = str(round(x / float(y) * 100, 1)) if y != 0 else "0" | |
| 542 return (str(x), str(y), z) | |
| 543 | |
| 544 dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount} | |
| 545 arr = ["RGYW", "WRCY", "WA", "TW"] | |
| 546 | |
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547 for fname in list(funcs.keys()): |
| 81 | 548 func = funcs[fname] |
| 549 foutfile = outfile[:outfile.rindex("/")] + "/hotspot_analysis_" + fname + ".txt" | |
| 550 with open(foutfile, 'w') as o: | |
| 551 for typ in arr: | |
| 552 o.write(typ + " (%)") | |
| 553 curr = dic[typ] | |
| 554 for gene in genes: | |
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555 if valuedic[gene + "_" + fname] == 0: |
| 81 | 556 o.write(",0,0,0") |
| 557 else: | |
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558 x, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.items() if z.startswith(gene)]], gene, func, fname) |
| 81 | 559 o.write("," + x + "," + y + "," + z) |
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560 x, y, z = get_xyz([y for x, y in curr.items() if not genedic[x].startswith("unmatched")], "total", func, fname) |
| 81 | 561 #x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname) |
| 562 o.write("," + x + "," + y + "," + z + "\n") | |
| 563 | |
| 564 | |
| 565 # for testing | |
| 566 seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt" | |
| 567 with open(seq_motif_file, 'w') as o: | |
| 568 o.write("ID\tRGYW\tWRCY\tWA\tTW\n") | |
| 569 for ID in IDlist: | |
| 570 #o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str(round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n") | |
| 571 o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n") | |
| 572 | |
| 573 if __name__ == "__main__": | |
| 574 main() |