gocli

gocli - GenomOncology Command Line Interface

This is a proprietary package that is available from GenomOncology and works with our Knowledge Management System.

For more information about licensing please contact us at:

[e-mail]

Additional proprietary projects available for download via pypi include:

• GO VCF - GenomOncology Variant Call File "call" generator
• GO SDK - GenomOncology Software Development Kit

Our open source projects include:

• Related - Nested Object Models in Python with dictionary, YAML, and JSON transformation support
• Specd - Swagger v2 Specification Directories
• Rigor - HTTP-based DSL for for validating RESTful APIs

Overview

The GenomOncology Command Line Interface (CLI) is a command line tool built to be dropped into Bioinformatics pipelines. GO CLI is a "high performance" ETL tool that understands genomics and directly integrates with the GO KMS via REST API calls for the following functionality:

• Variant HGVS Calculation (g., p., c.)
• Variant Annotation (e.g. gnomAD, dbSNP, etc.)
• Variant Classification (e.g. ACGM or AMP Tiers)
• Gene and Protein Information
• Clinical Trial Matching
• Therapeutic Matching
• Variant Warehouse Loading and Querying

High Performance

"High performance" is achieved through functional programming that minimizes memory consumption and asynchronous programming style (async/await, asyncio) that maximizes concurrency in high IO situations.

Examples

Generate BED file from List of Genes

gocli genes.txt genes.bed annotate_genes to_tsv

Filter VCF by BED, Filters, Quality, Mutation Type, and Population Frequency

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

Commands

$ 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.
  aggregate_genie_diseases  aggregates GENIE gene records.
  annotate_calls       Get annotations for stream of calls.
  annotate_genes       Get gene objects by stream of names.
  annotate_match       Get annotations for CSRA.
  annotate_match_bed   Get annotations for gene(s).
  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.