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:
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.
3 maintainers
Metadata
3 maintainers
Release files for gocli 0.12.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gocli-0.12.0.tar.gz | 87.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gocli-0.12.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 210.2 kB
Release files / gocli-0.12.0.tar.gz
| Download URL | gocli-0.12.0.tar.gz |
|---|---|
| Size | 87.5 kB |
| Tags | Source |
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|---|---|
| Size | 122.7 kB |
| Tags | Python 3 |
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