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gocli

Project description

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:

info@genomoncology.com

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. 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.

[GenomOncology]: https://genomoncology.com/ [Knowledge Management System]: https://genomoncology.com/solutions/clinical-oncology/ [Related]: https://github.com/genomoncology/related [Specd]: https://github.com/genomoncology/specd [Rigor]: https://github.com/genomoncology/rigor [GO VCF]: https://pypi.org/project/govcf/ [GO SDK]: https://pypi.org/project/gosdk/

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