本文整理汇总了Python中utilities.Utilities.patient_id_to_family方法的典型用法代码示例。如果您正苦于以下问题：Python Utilities.patient_id_to_family方法的具体用法？Python Utilities.patient_id_to_family怎么用？Python Utilities.patient_id_to_family使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类utilities.Utilities的用法示例。
在下文中一共展示了Utilities.patient_id_to_family方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: CompoundHets
# 需要导入模块: from utilities import Utilities [as 别名]
# 或者: from utilities.Utilities import patient_id_to_family [as 别名]
#.........这里部分代码省略.........
gene_list.append(variant.gene)
# Keep a lookback of 5 genes to account for gene overlaps
if len(current_genes) > self.lookback:
to_process = gene_list.pop(0)
self.process_gene(current_genes[to_process])
del current_genes[to_process]
current_genes[variant.gene].append(variant)
for gene in current_genes:
self.process_gene(current_genes[gene])
# Get any het calls for a gene and print the results
# Input:
# gene: A list of variants (Variant objects) within a gene
# Return:
# Nothing
def process_gene(self, gene):
if self.debug:
print("Processing gene")
hets = self.check_gene(gene)
if hets:
self.print_hets(hets)
# For each gene in the gene list, check whether each sample has a compound het pair within the gene
# Input:
# genes: dictionary of lists of Variants
# Return:
# samples: dictionary of lists of tuples of Variants
# positions: A list of tuples of variants
def check_gene(self, gene):
hets = []
identified_pairs = []
for v1 in gene:
for patient_id in v1.from_father_affected + v1.from_father_unaffected:
family_id = self.Utils.patient_id_to_family(patient_id)
if not self.families[family_id].members[patient_id].has_disease():
continue
for v2 in gene:
if v1.pos == v2.pos:
continue
if v2.has_maternal(patient_id):
key = "-".join(sorted([v1.pos, v2.pos, self.Utils.patient_id_to_family(patient_id)]))
het = CompoundHet(patient_id, v2, v1, self.families)
if not key in identified_pairs:
if self.transcript:
if v1.transcript == v2.transcript:
hets.append(het)
identified_pairs.append(key)
else:
hets.append(het)
identified_pairs.append(key)
return hets
# Print out the hets - debugging function
# input:
# hets: a CompoundHet object
def print_hets(self, hets):
for h in hets:
h.print_aggregate(self.aggregate_file)
h.print_family(self.output, self.prefix)
# Create output folder and initialize all output files with headers
# input:
# output: the output directory
# families: A dictionary of Family objects. Family IDs are the keys of the dictionary.
def setup_output(self, output, families):
# Due to popular demand this has been removed.