Metadata-Version: 1.1
Name: gocli
Version: 0.9.10
Summary: gocli
Home-page: UNKNOWN
Author: Ian Maurer
Author-email: ian@genomoncology.com
License: Proprietary
Description: 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.
              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/
        
        
        
Keywords: Bioinformatics HGVS VCF Clinical Trials Genomics
Platform: UNKNOWN
Classifier: License :: Other/Proprietary License
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
