Package: gocli
gocli - GenomOncology Command Line InterfaceThis is a proprietary package that is available fromGenomOncologyand works
with ourKnowledge Management System.For more information about licensing please contact us at:info@genomoncology.comAdditional proprietary projects available for download via pypi include:GO VCF- GenomOncology Variant Call File "call" generatorGO SDK- GenomOncology Software Development KitOur open source projects include:Related- Nested Object Models in Python with dictionary, YAML, and JSON transformation supportSpecd- Swagger v2 Specification DirectoriesRigor- HTTP-based DSL for for validating RESTful APIsOverviewThe 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 InformationClinical Trial MatchingTherapeutic MatchingVariant Warehouse Loading and QueryingHigh 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.ExamplesGenerate BED file from List of Genesgocli genes.txt genes.bed annotate_genes to_tsvFilter VCF by BED, Filters, Quality, Mutation Type, and Population Frequencygocli 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_vcfCommands$ 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.