e06b04eacb0eefdd392e54a0ec2a4f24c22ef50c,cnvlib/target.py,,assign_names,#Any#Any#Any#,59
Before Change
Replace the interval gene names with those at the same loc in refFlat.txt
ref_genes = read_refflat_genes(refflat_fname)
region_rows = sorted(region_rows,
key=lambda row: (row[0 ], row[3 ], row[1 ], row[2 ]))
for (chrom, strand), chr_rows in groupby (region_rows,
lambda row: (row[0 ], row[3 ]) ):
if (chrom, strand) not in ref_genes:
ngfrills.echo ("Chromosome" , chrom, "strand" , strand,
"not in annotations" )
continue
genes_in_chrom = iter(ref_genes[(chrom, strand)])
ex_start, ex_end, ex_name = next(genes_in_chrom)
for row in chr_rows:
start, end = row[1 :3 ]
After Change
if (chrom, std) in ref_genes:
strands_with_genes.extend(ref_genes[(chrom, std)])
if strands_with_genes:
genes_in_chrom = iter(sorted(strands_with_genes))
else :
ngfrills.echo("Chromosome" , chrom, strand, "not in annotations" )
continue
else :
In pattern: SUPERPATTERN
Frequency: 3
Non-data size: 5
Instances Project Name: etal/cnvkit
Commit Name: e06b04eacb0eefdd392e54a0ec2a4f24c22ef50c
Time: 2014-09-08
Author: eric.talevich@gmail.com
File Name: cnvlib/target.py
Class Name:
Method Name: assign_names
Project Name: pantsbuild/pants
Commit Name: 991b6233b442369be2310ca58fbd7c4b93f72c89
Time: 2014-12-23
Author: tinystatemachine@gmail.com
File Name: src/python/pants/backend/core/tasks/what_changed.py
Class Name: WhatChanged
Method Name: console_output
Project Name: pfnet/optuna
Commit Name: 6165fc267993ef3b58ca918f623a7e344729e6dd
Time: 2020-02-27
Author: hiroyuki.vincent.yamazaki@gmail.com
File Name: optuna/importance/_fanova.py
Class Name:
Method Name: _get_distributions