src.serena.analysis.investigator
File for class for analysis stuff
1#pylint: disable=line-too-long, too-few-public-methods, too-many-instance-attributes, too-many-locals,bare-except,invalid-name 2""" 3File for class for analysis stuff 4""" 5 6from typing import List 7from dataclasses import dataclass 8import attrs 9 10from serena.utilities.comparison_structures import ComparisonNucResults 11from serena.utilities.local_minima_variation import ComparisonLMVResponse 12 13@dataclass 14class SettingsAssertionLMV(): 15 """ 16 Settings use by algortihm that determines 17 what side of switch is asserted based on lmv_m 18 and lmv_c comparisons 19 """ 20 diff_limit_mfe:float = 0 21 """ The limt that the delta of lmv_c minus lmnv_m must be greater than """ 22 diff_limit_comp:float = 1 23 """ The limt that the delta of lmv_m minus lmnv_c must be greater than """ 24 25#@dataclass 26@attrs.define 27class LMVAssertionResult(): 28 """ 29 Results from LVM comparisons 30 """ 31 comp_compare_to_mfe:List[str] = [] 32 """ the lmv_c to lmv_m comparision as a <, >, or = symbol for each energy group""" 33 unbouund_pronounced:List[bool] = [] 34 """ A bool that indicates if that energy group has the unbound state pronounced via lmv comparisons """ 35 bound_pronounced: List[bool] = [] 36 """ A bool that indicates if that energy group has the bound state pronounced via lmv comparisons """ 37 is_on_off_switch:List[bool] = [] 38 """ List of Bools that indicates if that energy group has indications that it is a on/off switch based on lmv comparisons in enemble 39 A list is sued so tath the amount of on/off can be judged 40 """ 41 42#@dataclass 43#class SwitchabilitySettings(): 44# limit: float = 1.5 45 46#@dataclass 47#class SwitchynessResult(): 48# is_switchable_group:List[bool] 49# switchable_groups_list:List[int] 50# is_powerfull_switch_group:List[bool] 51# powerfull_groups_list:List[int] 52 53@dataclass 54class RatioResults(): 55 """ 56 Ratios for the comparison structure under analysis 57 """ 58 unbound_to_total_ratio:float = -1 59 bound_ratio: float = -1 60 last_unbound_ratio: float = -1 61 last_bound_ratio: float = -1 62 last_both_ratio: float = -1 63 bound_to_both_ratio: float = -1 64 bound_to_total_ratio:float = -1 65 both_nuc_total:float = -1 66 dot_to_total_ratio: float = -1 67 unbound_to_both:float = -1 68 69@attrs.define 70class ComparisonEvalResults(): 71 """ 72 Results from comparsion structure eval for ensemble by group 73 """ 74 #last_count_unbound:float=0 75 #last_count_bound:float=0 76 #last_count_both: float = 0 77 ratios:List[RatioResults] = [] 78 BRaise_list:List[float] =[] 79 BUratio_list:List[float] = [] 80 bound_total_list: List[int] = [] 81 unbound_total_list: List[int] = [] 82 nuc_penatly_count:int = 0 83 first_BUratio:float = 0 84 85@dataclass 86class InvestigatorResults(): 87 """ 88 Hold the results from the investigation by the investigator 89 this includes all the evidence so to speak that back up the 90 claims 91 """ 92 comparison_eval_results: ComparisonEvalResults 93 comp_nuc_counts: ComparisonNucResults 94 lmv_values: ComparisonLMVResponse 95 lmv_assertions: LMVAssertionResult 96 num_groups:int = 0 97 total_structures_ensemble:int = 0 98 99class ComparisonInvestigator(): 100 """ 101 The investigator for comparison algorithm to determine if 102 the comparison structures indicate that a RNA sequence is 103 capabale of acting as a switch 104 """ 105 def __init__(self) -> None: 106 pass 107 108 def evalulate_comparison_nucs(self, comparison_nucs:ComparisonNucResults)->ComparisonEvalResults:#pylint: disable=too-many-branches,too-many-statements 109 """ 110 Evaluate the results from the comparison nucs steps and return 111 the findings 112 """ 113 BRaise_list:List[float] = [] 114 BUratio_list:List[float] = [] 115 bound_total_list: List[int] = [] 116 unbound_total_list: List[int] = [] 117 ratios:List[RatioResults] = [] 118 nuc_penatly_count:int = 0 119 bound_hold:int = -1 120 for group_index in range(len(comparison_nucs.comparison_nuc_counts)):#pylint: disable=consider-using-enumerate 121 last_index:int = 0 122 if group_index > 0: 123 last_index = group_index -1 124 unbound:float = comparison_nucs.comparison_nuc_counts[group_index].unbound_count 125 last_unbound:float = comparison_nucs.comparison_nuc_counts[last_index].unbound_count 126 127 bound:float = comparison_nucs.comparison_nuc_counts[group_index].bound_count 128 last_bound:float = comparison_nucs.comparison_nuc_counts[last_index].bound_count 129 130 both_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].both_count 131 last_both:float = comparison_nucs.comparison_nuc_counts[last_index].both_count 132 133 dot_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].dot_count 134 135 nuc_count:int = comparison_nucs.comparison_nuc_counts[last_index].num_nucs 136 137 unbound_to_total_ratio:float = 0 138 bound_to_total_ratio:float = 0 139 both_nuc_total:float = 0 140 bound_ratio: float = 0 141 last_unbound_ratio = 0 142 last_bound_ratio = 0 143 last_both_ratio = 0 144 bound_to_both_ratio = 0 145 unbound_to_both_ratio = 0 146 try: 147 last_unbound_ratio = last_unbound/unbound 148 except: 149 pass 150 151 try: 152 bound_ratio = bound/unbound 153 except: 154 pass 155 156 try: 157 158 if bound_hold != -1: 159 #do normal 160 if bound_hold < last_bound: 161 if bound_hold == 0: 162 bound_hold = 1 163 last_bound_ratio = bound/bound_hold 164 else: 165 last_bound_ratio = bound/last_bound 166 else: 167 last_bound_ratio = bound/last_bound 168 169 if bound > last_bound: 170 #its getting bigger so record that 171 bound_hold = last_bound 172 else: 173 bound_hold = -1 174 except: 175 pass 176 177 #added to address the ones with 0 in the first group 178 if group_index > 0: 179 if BRaise_list[group_index-1] == 0 and bound > 0: 180 last_bound_ratio = bound 181 182 183 try: 184 last_both_ratio = both_nuc/last_both 185 except: 186 pass 187 188 try: 189 unbound_to_both_ratio = unbound/both_nuc 190 except: 191 pass 192 193 try: 194 bound_to_both_ratio = bound/(both_nuc - unbound) 195 except: 196 pass 197 198 unbound_to_total_ratio = unbound/nuc_count 199 bound_to_total_ratio = bound/nuc_count 200 both_nuc_total= both_nuc/nuc_count 201 dot_nuc_total= dot_nuc/nuc_count 202 203 bound_total_list.append(bound_to_total_ratio) 204 unbound_total_list.append(unbound_to_total_ratio) 205 206 #now round teh data to make it more managable 207 last_unbound_ratio = round(last_unbound_ratio,2) 208 last_bound_ratio = round(last_bound_ratio,2) 209 unbound_to_total_ratio = round(unbound_to_total_ratio,2) 210 bound_ratio = round(bound_ratio,2) 211 #bound_stats: str = f'BURatio:{round(bound_ratio,2)},both_Raise:{round(last_both_ratio,2)} BRaise:{round(last_bound_ratio,2)}, UDrop:{round(last_unbound_ratio,2)},BothTotal:{round(both_nuc_total,2)}, BoundTotal:{round(bound_to_total_ratio,2)}, UTotal:{round(unbound_to_total_ratio,2)}, bound_both:{round(bound_to_both_ratio,2)} B:{bound}, U:{unbound}. both:{both_nuc}' 212 213 214 #this is only for the fist kcal group 215 if group_index == 0: 216 nuc_penatly_count = bound 217 first_BUratio = round(bound_ratio,2) 218 219 BUratio_list.append(round(bound_ratio,2)) 220 BRaise_list.append(round(bound,2)) 221 222 ratio_results:RatioResults = RatioResults(unbound_to_total_ratio=unbound_to_total_ratio, 223 bound_ratio=bound_ratio, 224 last_unbound_ratio=last_unbound_ratio, 225 last_bound_ratio=last_bound_ratio, 226 last_both_ratio=last_both_ratio, 227 bound_to_both_ratio=bound_to_both_ratio, 228 bound_to_total_ratio=bound_to_total_ratio, 229 both_nuc_total=both_nuc_total, 230 dot_to_total_ratio=dot_nuc_total, 231 unbound_to_both=unbound_to_both_ratio 232 ) 233 ratios.append(ratio_results) 234 235 comparison_eval_results: ComparisonEvalResults = ComparisonEvalResults(ratios=ratios, 236 BRaise_list=BRaise_list, 237 BUratio_list=BUratio_list, 238 bound_total_list=bound_total_list, 239 unbound_total_list=unbound_total_list, 240 nuc_penatly_count=nuc_penatly_count, 241 first_BUratio=first_BUratio) 242 return comparison_eval_results 243 244class LocalMinimaVariationInvestigator(): 245 """ 246 Investigators for local minima variation results and whether 247 the lmv's of the ensemble groups indicate that the rna sequence is 248 capable of performing as a switch 249 """ 250 def __init__(self) -> None: 251 pass 252 253 def evaluate_lmv_for_structure_presence(self, lmv_data:ComparisonLMVResponse, setting:SettingsAssertionLMV)->LMVAssertionResult: 254 """ 255 Evalute the comparison structures lmv values and determine 256 if the enembled groups indicate a on/off switch. return the proof for 257 this determination as well for the judges to review 258 """ 259 ev_comp_limit: float = 25#25 260 ev_mfe_limit:float = 30 261 262 diff_limit_mfe:float = setting.diff_limit_mfe 263 diff_limit_comp:float = setting.diff_limit_comp 264 ev_min_limit:float = 30#15 265 266 comp_pronounced:List[bool] = [] 267 is_on_off_switch:List[bool] = [] 268 mfe_pronounced:List[bool] = [] 269 270 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 271 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 272 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 273 274 comp_asserted:bool = False 275 276 mfe_asserted:bool = False 277 278 """""" 279 diff_comp:float = round(ev_mfe,2) - round(ev_comp,2) 280 if round(ev_comp,1) < round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 281 #new stuff 282 if group_index > 0: 283 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 284 mfe_asserted = True 285 else: 286 if round(ev_comp,2) < 15 and round(ev_mfe,2) < 15: 287 mfe_asserted = True 288 289 elif round(ev_comp,1) == round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 290 #new stuff 291 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 292 mfe_asserted = True 293 comp_asserted = True 294 295 diff_mfe = round(ev_comp,2) - round(ev_mfe,2) 296 if round(ev_mfe,2) < round(ev_comp,2):# and (diff_mfe >= diff_limit_comp): 297 #new stuff 298 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 299 comp_asserted = True 300 301 if group_index > 0 and comp_asserted is True: 302 if mfe_pronounced[0] is True: 303 is_on_off_switch.append(True) 304 else: 305 is_on_off_switch.append(False) 306 307 comp_pronounced.append(comp_asserted) 308 mfe_pronounced.append(mfe_asserted) 309 310 ev_comp_to_mfe_list:List[str] = self.comp_compared_mfe_lmv(lmv_data=lmv_data) 311 312 lmv_presence_result: LMVAssertionResult = LMVAssertionResult(comp_compare_to_mfe=ev_comp_to_mfe_list, 313 unbouund_pronounced=mfe_pronounced, 314 bound_pronounced=comp_pronounced, 315 is_on_off_switch=is_on_off_switch) 316 317 return lmv_presence_result 318 319 def comp_compared_mfe_lmv(self, lmv_data:ComparisonLMVResponse)->List[str]: 320 """ 321 Determine if the lmv_c or lmv_m is asserted per group 322 """ 323 ev_comp_to_mfe_list:List[str] = [] 324 325 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 326 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 327 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 328 if ev_comp < ev_mfe: 329 ev_comp_to_mfe_list.append('<') 330 elif ev_comp == ev_mfe: 331 ev_comp_to_mfe_list.append('=') 332 elif ev_comp > ev_mfe: 333 ev_comp_to_mfe_list.append('>') 334 335 return ev_comp_to_mfe_list
@dataclass
class
SettingsAssertionLMV:
14@dataclass 15class SettingsAssertionLMV(): 16 """ 17 Settings use by algortihm that determines 18 what side of switch is asserted based on lmv_m 19 and lmv_c comparisons 20 """ 21 diff_limit_mfe:float = 0 22 """ The limt that the delta of lmv_c minus lmnv_m must be greater than """ 23 diff_limit_comp:float = 1 24 """ The limt that the delta of lmv_m minus lmnv_c must be greater than """
Settings use by algortihm that determines what side of switch is asserted based on lmv_m and lmv_c comparisons
@attrs.define
class
LMVAssertionResult:
27@attrs.define 28class LMVAssertionResult(): 29 """ 30 Results from LVM comparisons 31 """ 32 comp_compare_to_mfe:List[str] = [] 33 """ the lmv_c to lmv_m comparision as a <, >, or = symbol for each energy group""" 34 unbouund_pronounced:List[bool] = [] 35 """ A bool that indicates if that energy group has the unbound state pronounced via lmv comparisons """ 36 bound_pronounced: List[bool] = [] 37 """ A bool that indicates if that energy group has the bound state pronounced via lmv comparisons """ 38 is_on_off_switch:List[bool] = [] 39 """ List of Bools that indicates if that energy group has indications that it is a on/off switch based on lmv comparisons in enemble 40 A list is sued so tath the amount of on/off can be judged 41 """
Results from LVM comparisons
LMVAssertionResult( comp_compare_to_mfe: List[str] = [], unbouund_pronounced: List[bool] = [], bound_pronounced: List[bool] = [], is_on_off_switch: List[bool] = [])
2def __init__(self, comp_compare_to_mfe=attr_dict['comp_compare_to_mfe'].default, unbouund_pronounced=attr_dict['unbouund_pronounced'].default, bound_pronounced=attr_dict['bound_pronounced'].default, is_on_off_switch=attr_dict['is_on_off_switch'].default): 3 self.comp_compare_to_mfe = comp_compare_to_mfe 4 self.unbouund_pronounced = unbouund_pronounced 5 self.bound_pronounced = bound_pronounced 6 self.is_on_off_switch = is_on_off_switch
Method generated by attrs for class LMVAssertionResult.
comp_compare_to_mfe: List[str]
the lmv_c to lmv_m comparision as a <, >, or = symbol for each energy group
unbouund_pronounced: List[bool]
A bool that indicates if that energy group has the unbound state pronounced via lmv comparisons
@dataclass
class
RatioResults:
54@dataclass 55class RatioResults(): 56 """ 57 Ratios for the comparison structure under analysis 58 """ 59 unbound_to_total_ratio:float = -1 60 bound_ratio: float = -1 61 last_unbound_ratio: float = -1 62 last_bound_ratio: float = -1 63 last_both_ratio: float = -1 64 bound_to_both_ratio: float = -1 65 bound_to_total_ratio:float = -1 66 both_nuc_total:float = -1 67 dot_to_total_ratio: float = -1 68 unbound_to_both:float = -1
Ratios for the comparison structure under analysis
RatioResults( unbound_to_total_ratio: float = -1, bound_ratio: float = -1, last_unbound_ratio: float = -1, last_bound_ratio: float = -1, last_both_ratio: float = -1, bound_to_both_ratio: float = -1, bound_to_total_ratio: float = -1, both_nuc_total: float = -1, dot_to_total_ratio: float = -1, unbound_to_both: float = -1)
@attrs.define
class
ComparisonEvalResults:
70@attrs.define 71class ComparisonEvalResults(): 72 """ 73 Results from comparsion structure eval for ensemble by group 74 """ 75 #last_count_unbound:float=0 76 #last_count_bound:float=0 77 #last_count_both: float = 0 78 ratios:List[RatioResults] = [] 79 BRaise_list:List[float] =[] 80 BUratio_list:List[float] = [] 81 bound_total_list: List[int] = [] 82 unbound_total_list: List[int] = [] 83 nuc_penatly_count:int = 0 84 first_BUratio:float = 0
Results from comparsion structure eval for ensemble by group
ComparisonEvalResults( ratios: List[src.serena.analysis.investigator.RatioResults] = [], BRaise_list: List[float] = [], BUratio_list: List[float] = [], bound_total_list: List[int] = [], unbound_total_list: List[int] = [], nuc_penatly_count: int = 0, first_BUratio: float = 0)
2def __init__(self, ratios=attr_dict['ratios'].default, BRaise_list=attr_dict['BRaise_list'].default, BUratio_list=attr_dict['BUratio_list'].default, bound_total_list=attr_dict['bound_total_list'].default, unbound_total_list=attr_dict['unbound_total_list'].default, nuc_penatly_count=attr_dict['nuc_penatly_count'].default, first_BUratio=attr_dict['first_BUratio'].default): 3 self.ratios = ratios 4 self.BRaise_list = BRaise_list 5 self.BUratio_list = BUratio_list 6 self.bound_total_list = bound_total_list 7 self.unbound_total_list = unbound_total_list 8 self.nuc_penatly_count = nuc_penatly_count 9 self.first_BUratio = first_BUratio
Method generated by attrs for class ComparisonEvalResults.
ratios: List[src.serena.analysis.investigator.RatioResults]
@dataclass
class
InvestigatorResults:
86@dataclass 87class InvestigatorResults(): 88 """ 89 Hold the results from the investigation by the investigator 90 this includes all the evidence so to speak that back up the 91 claims 92 """ 93 comparison_eval_results: ComparisonEvalResults 94 comp_nuc_counts: ComparisonNucResults 95 lmv_values: ComparisonLMVResponse 96 lmv_assertions: LMVAssertionResult 97 num_groups:int = 0 98 total_structures_ensemble:int = 0
Hold the results from the investigation by the investigator this includes all the evidence so to speak that back up the claims
InvestigatorResults( comparison_eval_results: src.serena.analysis.investigator.ComparisonEvalResults, comp_nuc_counts: serena.utilities.comparison_structures.ComparisonNucResults, lmv_values: serena.utilities.local_minima_variation.ComparisonLMVResponse, lmv_assertions: src.serena.analysis.investigator.LMVAssertionResult, num_groups: int = 0, total_structures_ensemble: int = 0)
comparison_eval_results: src.serena.analysis.investigator.ComparisonEvalResults
lmv_assertions: src.serena.analysis.investigator.LMVAssertionResult
class
ComparisonInvestigator:
100class ComparisonInvestigator(): 101 """ 102 The investigator for comparison algorithm to determine if 103 the comparison structures indicate that a RNA sequence is 104 capabale of acting as a switch 105 """ 106 def __init__(self) -> None: 107 pass 108 109 def evalulate_comparison_nucs(self, comparison_nucs:ComparisonNucResults)->ComparisonEvalResults:#pylint: disable=too-many-branches,too-many-statements 110 """ 111 Evaluate the results from the comparison nucs steps and return 112 the findings 113 """ 114 BRaise_list:List[float] = [] 115 BUratio_list:List[float] = [] 116 bound_total_list: List[int] = [] 117 unbound_total_list: List[int] = [] 118 ratios:List[RatioResults] = [] 119 nuc_penatly_count:int = 0 120 bound_hold:int = -1 121 for group_index in range(len(comparison_nucs.comparison_nuc_counts)):#pylint: disable=consider-using-enumerate 122 last_index:int = 0 123 if group_index > 0: 124 last_index = group_index -1 125 unbound:float = comparison_nucs.comparison_nuc_counts[group_index].unbound_count 126 last_unbound:float = comparison_nucs.comparison_nuc_counts[last_index].unbound_count 127 128 bound:float = comparison_nucs.comparison_nuc_counts[group_index].bound_count 129 last_bound:float = comparison_nucs.comparison_nuc_counts[last_index].bound_count 130 131 both_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].both_count 132 last_both:float = comparison_nucs.comparison_nuc_counts[last_index].both_count 133 134 dot_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].dot_count 135 136 nuc_count:int = comparison_nucs.comparison_nuc_counts[last_index].num_nucs 137 138 unbound_to_total_ratio:float = 0 139 bound_to_total_ratio:float = 0 140 both_nuc_total:float = 0 141 bound_ratio: float = 0 142 last_unbound_ratio = 0 143 last_bound_ratio = 0 144 last_both_ratio = 0 145 bound_to_both_ratio = 0 146 unbound_to_both_ratio = 0 147 try: 148 last_unbound_ratio = last_unbound/unbound 149 except: 150 pass 151 152 try: 153 bound_ratio = bound/unbound 154 except: 155 pass 156 157 try: 158 159 if bound_hold != -1: 160 #do normal 161 if bound_hold < last_bound: 162 if bound_hold == 0: 163 bound_hold = 1 164 last_bound_ratio = bound/bound_hold 165 else: 166 last_bound_ratio = bound/last_bound 167 else: 168 last_bound_ratio = bound/last_bound 169 170 if bound > last_bound: 171 #its getting bigger so record that 172 bound_hold = last_bound 173 else: 174 bound_hold = -1 175 except: 176 pass 177 178 #added to address the ones with 0 in the first group 179 if group_index > 0: 180 if BRaise_list[group_index-1] == 0 and bound > 0: 181 last_bound_ratio = bound 182 183 184 try: 185 last_both_ratio = both_nuc/last_both 186 except: 187 pass 188 189 try: 190 unbound_to_both_ratio = unbound/both_nuc 191 except: 192 pass 193 194 try: 195 bound_to_both_ratio = bound/(both_nuc - unbound) 196 except: 197 pass 198 199 unbound_to_total_ratio = unbound/nuc_count 200 bound_to_total_ratio = bound/nuc_count 201 both_nuc_total= both_nuc/nuc_count 202 dot_nuc_total= dot_nuc/nuc_count 203 204 bound_total_list.append(bound_to_total_ratio) 205 unbound_total_list.append(unbound_to_total_ratio) 206 207 #now round teh data to make it more managable 208 last_unbound_ratio = round(last_unbound_ratio,2) 209 last_bound_ratio = round(last_bound_ratio,2) 210 unbound_to_total_ratio = round(unbound_to_total_ratio,2) 211 bound_ratio = round(bound_ratio,2) 212 #bound_stats: str = f'BURatio:{round(bound_ratio,2)},both_Raise:{round(last_both_ratio,2)} BRaise:{round(last_bound_ratio,2)}, UDrop:{round(last_unbound_ratio,2)},BothTotal:{round(both_nuc_total,2)}, BoundTotal:{round(bound_to_total_ratio,2)}, UTotal:{round(unbound_to_total_ratio,2)}, bound_both:{round(bound_to_both_ratio,2)} B:{bound}, U:{unbound}. both:{both_nuc}' 213 214 215 #this is only for the fist kcal group 216 if group_index == 0: 217 nuc_penatly_count = bound 218 first_BUratio = round(bound_ratio,2) 219 220 BUratio_list.append(round(bound_ratio,2)) 221 BRaise_list.append(round(bound,2)) 222 223 ratio_results:RatioResults = RatioResults(unbound_to_total_ratio=unbound_to_total_ratio, 224 bound_ratio=bound_ratio, 225 last_unbound_ratio=last_unbound_ratio, 226 last_bound_ratio=last_bound_ratio, 227 last_both_ratio=last_both_ratio, 228 bound_to_both_ratio=bound_to_both_ratio, 229 bound_to_total_ratio=bound_to_total_ratio, 230 both_nuc_total=both_nuc_total, 231 dot_to_total_ratio=dot_nuc_total, 232 unbound_to_both=unbound_to_both_ratio 233 ) 234 ratios.append(ratio_results) 235 236 comparison_eval_results: ComparisonEvalResults = ComparisonEvalResults(ratios=ratios, 237 BRaise_list=BRaise_list, 238 BUratio_list=BUratio_list, 239 bound_total_list=bound_total_list, 240 unbound_total_list=unbound_total_list, 241 nuc_penatly_count=nuc_penatly_count, 242 first_BUratio=first_BUratio) 243 return comparison_eval_results
The investigator for comparison algorithm to determine if the comparison structures indicate that a RNA sequence is capabale of acting as a switch
def
evalulate_comparison_nucs( self, comparison_nucs: serena.utilities.comparison_structures.ComparisonNucResults) -> src.serena.analysis.investigator.ComparisonEvalResults:
109 def evalulate_comparison_nucs(self, comparison_nucs:ComparisonNucResults)->ComparisonEvalResults:#pylint: disable=too-many-branches,too-many-statements 110 """ 111 Evaluate the results from the comparison nucs steps and return 112 the findings 113 """ 114 BRaise_list:List[float] = [] 115 BUratio_list:List[float] = [] 116 bound_total_list: List[int] = [] 117 unbound_total_list: List[int] = [] 118 ratios:List[RatioResults] = [] 119 nuc_penatly_count:int = 0 120 bound_hold:int = -1 121 for group_index in range(len(comparison_nucs.comparison_nuc_counts)):#pylint: disable=consider-using-enumerate 122 last_index:int = 0 123 if group_index > 0: 124 last_index = group_index -1 125 unbound:float = comparison_nucs.comparison_nuc_counts[group_index].unbound_count 126 last_unbound:float = comparison_nucs.comparison_nuc_counts[last_index].unbound_count 127 128 bound:float = comparison_nucs.comparison_nuc_counts[group_index].bound_count 129 last_bound:float = comparison_nucs.comparison_nuc_counts[last_index].bound_count 130 131 both_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].both_count 132 last_both:float = comparison_nucs.comparison_nuc_counts[last_index].both_count 133 134 dot_nuc:float = comparison_nucs.comparison_nuc_counts[group_index].dot_count 135 136 nuc_count:int = comparison_nucs.comparison_nuc_counts[last_index].num_nucs 137 138 unbound_to_total_ratio:float = 0 139 bound_to_total_ratio:float = 0 140 both_nuc_total:float = 0 141 bound_ratio: float = 0 142 last_unbound_ratio = 0 143 last_bound_ratio = 0 144 last_both_ratio = 0 145 bound_to_both_ratio = 0 146 unbound_to_both_ratio = 0 147 try: 148 last_unbound_ratio = last_unbound/unbound 149 except: 150 pass 151 152 try: 153 bound_ratio = bound/unbound 154 except: 155 pass 156 157 try: 158 159 if bound_hold != -1: 160 #do normal 161 if bound_hold < last_bound: 162 if bound_hold == 0: 163 bound_hold = 1 164 last_bound_ratio = bound/bound_hold 165 else: 166 last_bound_ratio = bound/last_bound 167 else: 168 last_bound_ratio = bound/last_bound 169 170 if bound > last_bound: 171 #its getting bigger so record that 172 bound_hold = last_bound 173 else: 174 bound_hold = -1 175 except: 176 pass 177 178 #added to address the ones with 0 in the first group 179 if group_index > 0: 180 if BRaise_list[group_index-1] == 0 and bound > 0: 181 last_bound_ratio = bound 182 183 184 try: 185 last_both_ratio = both_nuc/last_both 186 except: 187 pass 188 189 try: 190 unbound_to_both_ratio = unbound/both_nuc 191 except: 192 pass 193 194 try: 195 bound_to_both_ratio = bound/(both_nuc - unbound) 196 except: 197 pass 198 199 unbound_to_total_ratio = unbound/nuc_count 200 bound_to_total_ratio = bound/nuc_count 201 both_nuc_total= both_nuc/nuc_count 202 dot_nuc_total= dot_nuc/nuc_count 203 204 bound_total_list.append(bound_to_total_ratio) 205 unbound_total_list.append(unbound_to_total_ratio) 206 207 #now round teh data to make it more managable 208 last_unbound_ratio = round(last_unbound_ratio,2) 209 last_bound_ratio = round(last_bound_ratio,2) 210 unbound_to_total_ratio = round(unbound_to_total_ratio,2) 211 bound_ratio = round(bound_ratio,2) 212 #bound_stats: str = f'BURatio:{round(bound_ratio,2)},both_Raise:{round(last_both_ratio,2)} BRaise:{round(last_bound_ratio,2)}, UDrop:{round(last_unbound_ratio,2)},BothTotal:{round(both_nuc_total,2)}, BoundTotal:{round(bound_to_total_ratio,2)}, UTotal:{round(unbound_to_total_ratio,2)}, bound_both:{round(bound_to_both_ratio,2)} B:{bound}, U:{unbound}. both:{both_nuc}' 213 214 215 #this is only for the fist kcal group 216 if group_index == 0: 217 nuc_penatly_count = bound 218 first_BUratio = round(bound_ratio,2) 219 220 BUratio_list.append(round(bound_ratio,2)) 221 BRaise_list.append(round(bound,2)) 222 223 ratio_results:RatioResults = RatioResults(unbound_to_total_ratio=unbound_to_total_ratio, 224 bound_ratio=bound_ratio, 225 last_unbound_ratio=last_unbound_ratio, 226 last_bound_ratio=last_bound_ratio, 227 last_both_ratio=last_both_ratio, 228 bound_to_both_ratio=bound_to_both_ratio, 229 bound_to_total_ratio=bound_to_total_ratio, 230 both_nuc_total=both_nuc_total, 231 dot_to_total_ratio=dot_nuc_total, 232 unbound_to_both=unbound_to_both_ratio 233 ) 234 ratios.append(ratio_results) 235 236 comparison_eval_results: ComparisonEvalResults = ComparisonEvalResults(ratios=ratios, 237 BRaise_list=BRaise_list, 238 BUratio_list=BUratio_list, 239 bound_total_list=bound_total_list, 240 unbound_total_list=unbound_total_list, 241 nuc_penatly_count=nuc_penatly_count, 242 first_BUratio=first_BUratio) 243 return comparison_eval_results
Evaluate the results from the comparison nucs steps and return the findings
class
LocalMinimaVariationInvestigator:
245class LocalMinimaVariationInvestigator(): 246 """ 247 Investigators for local minima variation results and whether 248 the lmv's of the ensemble groups indicate that the rna sequence is 249 capable of performing as a switch 250 """ 251 def __init__(self) -> None: 252 pass 253 254 def evaluate_lmv_for_structure_presence(self, lmv_data:ComparisonLMVResponse, setting:SettingsAssertionLMV)->LMVAssertionResult: 255 """ 256 Evalute the comparison structures lmv values and determine 257 if the enembled groups indicate a on/off switch. return the proof for 258 this determination as well for the judges to review 259 """ 260 ev_comp_limit: float = 25#25 261 ev_mfe_limit:float = 30 262 263 diff_limit_mfe:float = setting.diff_limit_mfe 264 diff_limit_comp:float = setting.diff_limit_comp 265 ev_min_limit:float = 30#15 266 267 comp_pronounced:List[bool] = [] 268 is_on_off_switch:List[bool] = [] 269 mfe_pronounced:List[bool] = [] 270 271 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 272 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 273 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 274 275 comp_asserted:bool = False 276 277 mfe_asserted:bool = False 278 279 """""" 280 diff_comp:float = round(ev_mfe,2) - round(ev_comp,2) 281 if round(ev_comp,1) < round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 282 #new stuff 283 if group_index > 0: 284 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 285 mfe_asserted = True 286 else: 287 if round(ev_comp,2) < 15 and round(ev_mfe,2) < 15: 288 mfe_asserted = True 289 290 elif round(ev_comp,1) == round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 291 #new stuff 292 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 293 mfe_asserted = True 294 comp_asserted = True 295 296 diff_mfe = round(ev_comp,2) - round(ev_mfe,2) 297 if round(ev_mfe,2) < round(ev_comp,2):# and (diff_mfe >= diff_limit_comp): 298 #new stuff 299 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 300 comp_asserted = True 301 302 if group_index > 0 and comp_asserted is True: 303 if mfe_pronounced[0] is True: 304 is_on_off_switch.append(True) 305 else: 306 is_on_off_switch.append(False) 307 308 comp_pronounced.append(comp_asserted) 309 mfe_pronounced.append(mfe_asserted) 310 311 ev_comp_to_mfe_list:List[str] = self.comp_compared_mfe_lmv(lmv_data=lmv_data) 312 313 lmv_presence_result: LMVAssertionResult = LMVAssertionResult(comp_compare_to_mfe=ev_comp_to_mfe_list, 314 unbouund_pronounced=mfe_pronounced, 315 bound_pronounced=comp_pronounced, 316 is_on_off_switch=is_on_off_switch) 317 318 return lmv_presence_result 319 320 def comp_compared_mfe_lmv(self, lmv_data:ComparisonLMVResponse)->List[str]: 321 """ 322 Determine if the lmv_c or lmv_m is asserted per group 323 """ 324 ev_comp_to_mfe_list:List[str] = [] 325 326 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 327 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 328 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 329 if ev_comp < ev_mfe: 330 ev_comp_to_mfe_list.append('<') 331 elif ev_comp == ev_mfe: 332 ev_comp_to_mfe_list.append('=') 333 elif ev_comp > ev_mfe: 334 ev_comp_to_mfe_list.append('>') 335 336 return ev_comp_to_mfe_list
Investigators for local minima variation results and whether the lmv's of the ensemble groups indicate that the rna sequence is capable of performing as a switch
def
evaluate_lmv_for_structure_presence( self, lmv_data: serena.utilities.local_minima_variation.ComparisonLMVResponse, setting: src.serena.analysis.investigator.SettingsAssertionLMV) -> src.serena.analysis.investigator.LMVAssertionResult:
254 def evaluate_lmv_for_structure_presence(self, lmv_data:ComparisonLMVResponse, setting:SettingsAssertionLMV)->LMVAssertionResult: 255 """ 256 Evalute the comparison structures lmv values and determine 257 if the enembled groups indicate a on/off switch. return the proof for 258 this determination as well for the judges to review 259 """ 260 ev_comp_limit: float = 25#25 261 ev_mfe_limit:float = 30 262 263 diff_limit_mfe:float = setting.diff_limit_mfe 264 diff_limit_comp:float = setting.diff_limit_comp 265 ev_min_limit:float = 30#15 266 267 comp_pronounced:List[bool] = [] 268 is_on_off_switch:List[bool] = [] 269 mfe_pronounced:List[bool] = [] 270 271 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 272 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 273 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 274 275 comp_asserted:bool = False 276 277 mfe_asserted:bool = False 278 279 """""" 280 diff_comp:float = round(ev_mfe,2) - round(ev_comp,2) 281 if round(ev_comp,1) < round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 282 #new stuff 283 if group_index > 0: 284 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 285 mfe_asserted = True 286 else: 287 if round(ev_comp,2) < 15 and round(ev_mfe,2) < 15: 288 mfe_asserted = True 289 290 elif round(ev_comp,1) == round(ev_mfe,1):# and diff_comp >= diff_limit_mfe: 291 #new stuff 292 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 293 mfe_asserted = True 294 comp_asserted = True 295 296 diff_mfe = round(ev_comp,2) - round(ev_mfe,2) 297 if round(ev_mfe,2) < round(ev_comp,2):# and (diff_mfe >= diff_limit_comp): 298 #new stuff 299 if round(ev_comp,2) < ev_comp_limit and round(ev_mfe,2) < ev_mfe_limit: 300 comp_asserted = True 301 302 if group_index > 0 and comp_asserted is True: 303 if mfe_pronounced[0] is True: 304 is_on_off_switch.append(True) 305 else: 306 is_on_off_switch.append(False) 307 308 comp_pronounced.append(comp_asserted) 309 mfe_pronounced.append(mfe_asserted) 310 311 ev_comp_to_mfe_list:List[str] = self.comp_compared_mfe_lmv(lmv_data=lmv_data) 312 313 lmv_presence_result: LMVAssertionResult = LMVAssertionResult(comp_compare_to_mfe=ev_comp_to_mfe_list, 314 unbouund_pronounced=mfe_pronounced, 315 bound_pronounced=comp_pronounced, 316 is_on_off_switch=is_on_off_switch) 317 318 return lmv_presence_result
Evalute the comparison structures lmv values and determine if the enembled groups indicate a on/off switch. return the proof for this determination as well for the judges to review
def
comp_compared_mfe_lmv( self, lmv_data: serena.utilities.local_minima_variation.ComparisonLMVResponse) -> List[str]:
320 def comp_compared_mfe_lmv(self, lmv_data:ComparisonLMVResponse)->List[str]: 321 """ 322 Determine if the lmv_c or lmv_m is asserted per group 323 """ 324 ev_comp_to_mfe_list:List[str] = [] 325 326 for group_index in range(len(lmv_data.lmv_comps)):#pylint: disable=consider-using-enumerate 327 ev_comp:float = lmv_data.lmv_comps[group_index].lmv_comp.ev_normalized 328 ev_mfe:float = lmv_data.lmv_comps[group_index].lmv_mfe.ev_normalized 329 if ev_comp < ev_mfe: 330 ev_comp_to_mfe_list.append('<') 331 elif ev_comp == ev_mfe: 332 ev_comp_to_mfe_list.append('=') 333 elif ev_comp > ev_mfe: 334 ev_comp_to_mfe_list.append('>') 335 336 return ev_comp_to_mfe_list
Determine if the lmv_c or lmv_m is asserted per group