| Name | gocli JSON |
| Version |
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| home_page | None |
| Summary | gocli |
| upload_time | 2024-04-12 19:34:36 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.11 |
| license | None |
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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:
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.
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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"description": "gocli - GenomOncology Command Line Interface\n============================================\n\n\nThis is a proprietary package that is available from [GenomOncology] and works\nwith our [Knowledge Management System].\n\nFor more information about licensing please contact us at:\n\ninfo@genomoncology.com\n\n \nAdditional proprietary projects available for download via pypi include:\n\n* [GO VCF] - GenomOncology Variant Call File \"call\" generator\n* [GO SDK] - GenomOncology Software Development Kit\n \nOur open source projects include:\n\n* [Related] - Nested Object Models in Python with dictionary, YAML, and JSON transformation support\n* [Specd] - Swagger v2 Specification Directories\n* [Rigor] - HTTP-based DSL for for validating RESTful APIs\n\n\nOverview\n--------\n\nThe GenomOncology Command Line Interface (CLI) is a command line tool built to be\ndropped into Bioinformatics pipelines. GO CLI is a \"high performance\" ETL tool that\nunderstands genomics and directly integrates with the GO KMS via REST API calls\nfor the following functionality:\n\n* Variant HGVS Calculation (g., p., c.)\n* Variant Annotation (e.g. gnomAD, dbSNP, etc.)\n* Variant Classification (e.g. ACGM or AMP Tiers)\n* Gene and Protein Information\n* Clinical Trial Matching\n* Therapeutic Matching\n* Variant Warehouse Loading and Querying\n\n\nHigh Performance\n----------------\n\n\"High performance\" is achieved through functional programming that minimizes\nmemory consumption and asynchronous programming style (async/await, asyncio) that\nmaximizes concurrency in high IO situations.\n\n\n\nExamples\n--------\n\nGenerate BED file from List of Genes\n\n gocli genes.txt genes.bed annotate_genes to_tsv\n\n\nFilter VCF by BED, Filters, Quality, Mutation Type, and Population Frequency\n\n gocli demo_1.vcf demo_1.filtered.vcf \\\n from_vcf --bed=./snv_cancer.bed \\\n filter_in quality GTE 100 \\\n filter_in vaf GTE \"0.05\" \\\n annotate_calls \\\n retain \"annotations.clinvar__CLNSIG__string\" HAS \"Pathogenic\"\n filter_in annotations.canonical_mutation_type IN @mt.txt \\\n filter_out annotations.GNOMAD__AF__mfloat GT \"0.01\" \\\n to_vcf\n\n\nCommands\n--------\n\n $ gocli --help\n add_flag Add flag based on BED file value/presence.\n aggregate_csv Rolls up CSV records using a specified key.\n aggregate_tsv Rolls up TSV records using a specified key.\n annotate_calls Get annotations for stream of calls.\n annotate_genes Get gene objects by stream of names.\n annotate_match Get annotations for CSRA.\n annotate_match_bed Get annotations for gene(s).\n distinct Remove duplicates from a list of strings.\n extract Extract a specific field from object stream.\n filter_in Filter in objects that match comparison.\n filter_out Filter out objects that match comparison.\n flatten Flatten list of lists into a list of strings.\n from_bed Read records from a BED file source.\n from_csv Parses CSV into name-value pair objects.\n from_excel Parses Excel into name-value pair objects.\n from_maf Read records from a MAF file source.\n from_source Parse file into name-value pair objects.\n from_tsv Parses TSV into name-value pair objects.\n from_vcf Parses VCF into variant calls objects.\n invoke Invoke an external function.\n load_annotations Loads variant objects into annotations core.\n load_warehouse Loads variants to warehouse.\n match_contents Match contents by variants and disease.\n match_therapies Match therapies by variants and disease.\n match_trials Match trials by variants and disease.\n refresh_annotations Rebuilds annotations merged core.\n region_search Searches for Transcript in region specified...\n retain Always keep objects that match comparison.\n swagger Launches local Swagger UI webserver.\n to_excel Render objects to Excel file format.\n to_pretty Render indented, syntax highlighted JSON.\n to_python Render python objects without JSON transform.\n to_tsv Render objects to TSV file format.\n to_vcf Render calls to VCF file format.\n transform Transform input stream to output type.\n\n\n[GenomOncology]: https://genomoncology.com/\n[Knowledge Management System]: https://genomoncology.com/solutions/clinical-oncology/\n[Related]: https://github.com/genomoncology/related\n[Specd]: https://github.com/genomoncology/specd \n[Rigor]: https://github.com/genomoncology/rigor \n[GO VCF]: https://pypi.org/project/govcf/\n[GO SDK]: https://pypi.org/project/gosdk/\n",
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