本文整理汇总了Python中utilities.Utilities.parse_line方法的典型用法代码示例。如果您正苦于以下问题：Python Utilities.parse_line方法的具体用法？Python Utilities.parse_line怎么用？Python Utilities.parse_line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.parse_line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 parse_line [as 别名]
class CompoundHets(object):
def __init__(self, input, ped, frequency_cutoff=None, consequence=None, output=None, prefix=None, transcript=False, debug=False,
gene_lookback=5, force=False):
self.frequency_cutoff = frequency_cutoff
self.consequence = consequence
self.transcript = transcript
self.output = output
self.prefix = prefix
self.force = force
self.aggregate_file = os.path.join(output, 'compound_hets.aggregate.tsv')
if self.prefix:
self.aggregate_file = os.path.join(output, self.prefix + '.compound_hets.aggregate.tsv')
self.debug = debug
self.Utils = Utilities(self.frequency_cutoff, self.consequence, self.transcript, self.debug)
self.families = self.Utils.read_ped_file(ped)
self.lookback = gene_lookback
self.setup_output(output, self.families)
self.process_file(input)
# Print each compound het pair for each sample to a sample file
# Input:
# samples: dictionary of lists of tuples of Variants
# output: output prefix
def print_samples(self, samples, output):
if not samples:
return
for s in samples:
filename = "%s.compound_het_pairs.txt" % s
if self.prefix:
filename = self.prefix + "." + filename
if output:
filename = "%s.%s.compound_het_pairs.txt" % (output, s)
f = open(filename, 'w')
f.write("#PAIR\tCHR\tPOS\tGENE\n")
count = 1
for pair in samples[s]:
v1 = pair[0]
v2 = pair[1]
f.write(v1.for_sample_file(count) + "\n")
f.write(v2.for_sample_file(count) + "\n")
count += 1
f.close()
# Print all pairs of compound hets to file
# Input:
# positions: A list of tuples of variants
# output: output file prefix
def print_positions(self, positions, output):
if not positions:
return
filename = "all_compound_het_pairs.txt"
if output:
filename = "%s.all_compound_het_pairs.txt" % output
f = open(filename, 'w')
f.write("#PAIR\tCHR\tPOS\tGENE\tFROM_MOTHER\tFROM_FATHER\n")
count = 1
for p in positions:
v1 = p[0]
v2 = p[1]
f.write(v1.for_variant_file(count) + "\n")
f.write(v2.for_variant_file(count) + "\n")
count += 1
f.close()
# Parse each line in the input file, convert it to a Variant object, and assign it to a gene within the gene
# dictionary
# Input:
# input: input filename
# Return:
# genes: dictionary of lists of Variants
def process_file(self, input):
current_genes = defaultdict(list)
gene_list = []
checked_genes = []
with open(input) as f:
for line in f:
if line.startswith('#'):
continue
variant = self.Utils.parse_line(line)
if variant is None:
continue
if variant.gene not in current_genes:
if variant.gene in checked_genes:
print("%s ALREADY CHECKED! File may be out of order!" % variant.gene)
else:
checked_genes.append(variant.gene)
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
#.........这里部分代码省略.........