def is_pathogenic(templine, headlist, yaml_commands):
templinelist = templine.split("\t")
pathogenic = 0
tiering_cmds = yaml_commands[yaml_keys.kModules][yaml_keys.kTiering]
nalg = tiering_cmds[yaml_keys.kTPathogenicityGlobalThreshold]
colHeaders = yaml_utils.convertColumns(
tiering_cmds[yaml_keys.kTPathogenicityCols], yaml_commands)
colsThresholds = tiering_cmds[yaml_keys.kTPathogenicityThresholds]
for idx, colHeader in enumerate(colHeaders):
if (isinstance(colHeader, list)):
passed = False
colThresholdsList = colsThresholds[idx]
for idx, singleColHeader in enumerate(colHeader):
colThresholds = yaml_utils.split_multiple_col_thresholds(
colThresholdsList[idx], yaml_commands)
col = templinelist[headlist.index(singleColHeader)]
if (passes_criteria(col, colThresholds)):
passed = True
break
if (passed):
pathogenic += 1
continue
#else
colThresholds = yaml_utils.split_multiple_col_thresholds(
colsThresholds[idx], yaml_commands)
col = templinelist[headlist.index(colHeader)]
passed = passes_criteria(col, colThresholds)
if (passed):
pathogenic += 1
if pathogenic >= int(nalg):
#debug
# print 'is pathogenic'
return 1
else:
#debug
# print 'not pathogenic'
return 0
def is_pathogenic(templine, headlist, yaml_commands):
templinelist = templine.split("\t")
pathogenic = 0
tiering_cmds = yaml_commands[yaml_keys.kModules][yaml_keys.kTiering]
nalg = tiering_cmds[yaml_keys.kTPathogenicityGlobalThreshold]
colHeaders = yaml_utils.convertColumns(tiering_cmds[yaml_keys.kTPathogenicityCols], yaml_commands)
colsThresholds = tiering_cmds[yaml_keys.kTPathogenicityThresholds]
for idx,colHeader in enumerate(colHeaders):
if(isinstance(colHeader, list)):
passed = False
colThresholdsList = colsThresholds[idx]
for idx,singleColHeader in enumerate(colHeader):
colThresholds = yaml_utils.split_multiple_col_thresholds(colThresholdsList[idx], yaml_commands)
col = templinelist[headlist.index(singleColHeader)]
if(passes_criteria(col, colThresholds)):
passed = True
break
if(passed):
pathogenic += 1
continue
#else
colThresholds = yaml_utils.split_multiple_col_thresholds(colsThresholds[idx], yaml_commands)
col = templinelist[headlist.index(colHeader)]
passed = passes_criteria(col, colThresholds)
if(passed):
pathogenic += 1
if pathogenic >= int(nalg):
#debug
# print 'is pathogenic'
return 1
else:
#debug
# print 'not pathogenic'
return 0
def is_pathogenic(templine, headlist, yaml_commands):
templinelist = templine.split("\t")
pathogenic = 0
tiering_cmds = yaml_commands[yaml_keys.kModules][yaml_keys.kTiering]
nalg = tiering_cmds[yaml_keys.kTPathogenicityGlobalThreshold]
colHeaders = yaml_utils.convertColumns(tiering_cmds[yaml_keys.kTPathogenicityCols], yaml_commands)
colsThresholds = tiering_cmds[yaml_keys.kTPathogenicityThresholds]
for idx,colHeader in enumerate(colHeaders):
if(isinstance(colHeader, list)):
passed = False
colThresholdsList = colsThresholds[idx]
for idx,singleColHeader in enumerate(colHeader):
colThresholds = yaml_utils.split_multiple_col_thresholds(colThresholdsList[idx], yaml_commands)
col = templinelist[headlist.index(singleColHeader)]
if(passes_criteria(col, colThresholds)):
passed = True
break
if(passed):
pathogenic += 1
continue
#else
# if(isinstance(colsThresholds[idx], list)):
colThresholds = yaml_utils.split_multiple_col_thresholds(colsThresholds[idx], yaml_commands)
col = templinelist[headlist.index(colHeader)]
passed = passes_criteria(col, colThresholds)
if(passed):
pathogenic += 1
# passed = False
# for colThreshold in colThresholds:
# if(col != '' and
# (((type(colThreshold) is float or type(colThreshold) is int) and float(col) >= colThreshold)
# or col == colThreshold)
# ):
# passed = True
# break
# if(passed):
# pathogenic += 1
# sift = templinelist[headlist.index(vcfHeaders.kSiftPred)] if vcfHeaders.kSiftPred in headlist else ''
# pp2 = templinelist[headlist.index(vcfHeaders.kPolyphen2Pred)] if vcfHeaders.kPolyphen2Pred in headlist else ''
# lrt = templinelist[headlist.index(vcfHeaders.kLrtPred)] if vcfHeaders.kLrtPred in headlist else ''
# mt = templinelist[headlist.index(vcfHeaders.kMutationTasterPred)] if vcfHeaders.kMutationTasterPred in headlist else ''
# pp2_2 = templinelist[headlist.index(vcfHeaders.kPolyphen2Pred_2)] if vcfHeaders.kPolyphen2Pred_2 in headlist else ''
#
# # check for header mismatches
# if(vcfHeaders.kSiftPred not in headlist):
# print 'warning: ' + vcfHeaders.kSiftPred + ' not found in annotated header'
# if(vcfHeaders.kPolyphen2Pred not in headlist):
# print 'warning: ' + vcfHeaders.kPolyphen2Pred + ' not found in annotated header'
# if(vcfHeaders.kLrtPred not in headlist):
# print 'warning: ' + vcfHeaders.kLrtPred + ' not found in annotated header'
# if(vcfHeaders.kMutationTasterPred not in headlist):
# print 'warning: ' + vcfHeaders.kMutationTasterPred + ' not found in annotated header'
# if(vcfHeaders.kPolyphen2Pred_2 not in headlist):
# print 'warning: ' + vcfHeaders.kPolyphen2Pred_2 + ' not found in annotated header (though currently unused)'
#
# if sift == "D":
# pathogenic+=1
# #debug
# print 'SIFT=D'
# if (pp2 == "P") or (pp2 == "D"):
# pathogenic+=1
# #debug
# print 'pp=P or D'
# if lrt == "D":
# pathogenic+=1
# # debug
# print 'lrt=D'
# if (mt == "A") or (mt == "D"):
# pathogenic+=1
# #debug
# print 'mt=A or D'
if pathogenic >= int(nalg):
#debug
# print 'is pathogenic'
return 1
else:
#debug
# print 'not pathogenic'
return 0