gocli 0.9.2

概述

genomology命令行界面（cli）是为 投入到生物信息学的管道中。go cli是一个“高性能”etl工具 了解基因组学并通过rest api调用直接与go-kms集成 对于以下功能：

• 变量hgvs计算（g.，p.，c.）
• 变体注释（例如gnomad、dbsnp等）
• 变量分类（例如ACGM或AMP层）
• 基因和蛋白质信息
• 临床试验匹配
• 治疗匹配
• 变量仓库加载和查询

高性能

“高性能”是通过最小化 内存消耗和异步编程风格（async/await，asyncio） 在高IO情况下最大化并发性。

示例

从基因列表生成床文件

gocli genes.txt genes.bed annotate_genes to_tsv

按床、过滤器、质量、突变类型和群体频率过滤VCF

gocli demo_1.vcf demo_1.filtered.vcf

from_vcf –bed=./snv_cancer.bed filter_in quality GTE 100 filter_in vaf GTE “0.05” annotate_calls retain “annotations.clinvar__CLNSIG__string” HAS “Pathogenic” filter_in annotations.canonical_mutation_type IN @mt.txt filter_out annotations.GNOMAD__AF__mfloat GT “0.01” to_vcf

命令

$ gocli –help

add_flag Add flag based on BED file value/presence. aggregate_csv Rolls up CSV records using a specified key. aggregate_tsv Rolls up TSV records using a specified key. annotate_calls Get annotations for stream of calls. annotate_genes Get gene objects by stream of names. distinct Remove duplicates from a list of strings. extract Extract a specific field from object stream. filter_in Filter in objects that match comparison. filter_out Filter out objects that match comparison. flatten Flatten list of lists into a list of strings. from_bed Read records from a BED file source. from_csv Parses CSV into name-value pair objects. from_excel Parses Excel into name-value pair objects. from_maf Read records from a MAF file source. from_source Parse file into name-value pair objects. from_tsv Parses TSV into name-value pair objects. from_vcf Parses VCF into variant calls objects. invoke Invoke an external function. load_annotations Loads variant objects into annotations core. load_warehouse Loads variants to warehouse. match_contents Match contents by variants and disease. match_therapies Match therapies by variants and disease. match_trials Match trials by variants and disease. refresh_annotations Rebuilds annotations merged core. region_search Searches for Transcript in region specified… retain Always keep objects that match comparison. swagger Launches local Swagger UI webserver. to_excel Render objects to Excel file format. to_pretty Render indented, syntax highlighted JSON. to_python Render python objects without JSON transform. to_tsv Render objects to TSV file format. to_vcf Render calls to VCF file format. transform Transform input stream to output type.

[基因组学]：https://genomoncology.com/ [知识管理系统]：https://genomoncology.com/solutions/clinical-oncology/ [相关]：https://github.com/genomoncology/related [规格]：https://github.com/genomoncology/specd [严谨]：https://github.com/genomoncology/rigor [去vcf]：https://pypi.org/project/govcf/ [去sdk]：https://pypi.org/project/gosdk/