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:
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
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
Variant Warehouse Loading and Querying
“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.
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
- $ 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. 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.
[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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