Command Line Interface

The pysec2pri CLI provides easy commands for each supported database.

pysec2pri

pysec2pri – secondary-to-primary ID and label mapping.

Usage

pysec2pri [OPTIONS] COMMAND [ARGS]...

Options

--version: Show the version and exit.

all

Export all output formats for each listed datasource.

Usage

pysec2pri all [OPTIONS]

Options

-o, --output-dir <output_dir>: Output directory.

--datasources <datasources>

Comma-separated config IDs to export.

Default:: 'chebi,hgnc,ncbi,uniprot,wikidata,hmdb_metabolites,hmdb_proteins'

ambiguous

Find ambiguous mappings for DATASOURCE and save as SSSOM.

DATASOURCE format: <config-id>-<kind>, e.g. hgnc-ids, chebi-labels, hmdb-metabolites-ids, wikidata-labels.

Usage

pysec2pri ambiguous [OPTIONS] {chebi-ids|chebi-labels|hgnc-ids|hgnc-
                    labels|ncbi-ids|ncbi-labels|hmdb-metabolites-ids|hmdb-
                    proteins-ids|uniprot-ids|wikidata-ids|wikidata-labels}

Options

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--no-progress: Suppress progress bars.

Arguments

DATASOURCE: Required argument

chebi

ChEBI mappings.

Usage

pysec2pri chebi [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri chebi ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

--subset <subset>

Compound subset.

Default:: '3star'
Options:: 3star | complete

labels

Usage

pysec2pri chebi labels [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | label_sec2pri | name2synonym | pri_labels | rdf | json | owl | all

--no-progress: Suppress progress bars.

--subset <subset>

Compound subset.

Default:: '3star'
Options:: 3star | complete

diff

Compare two SSSOM mapping files and show differences.

Usage

pysec2pri diff [OPTIONS] FILE1 FILE2

Options

-o, --output <output>: Output file for diff results (TSV).

--show-all: Show all differences.

--datasource <datasource>: Datasource name for diff summary.

Arguments

FILE1: Required argument

FILE2: Required argument

hgnc

HGNC mappings.

Usage

pysec2pri hgnc [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri hgnc ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

labels

Usage

pysec2pri hgnc labels [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | label_sec2pri | name2synonym | pri_labels | rdf | json | owl | all

--no-progress: Suppress progress bars.

hmdb-metabolites

HMDB Metabolites mappings.

Usage

pysec2pri hmdb-metabolites [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri hmdb-metabolites ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

hmdb-proteins

HMDB Proteins mappings.

Usage

pysec2pri hmdb-proteins [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri hmdb-proteins ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

list-versions

List available archive versions for DATASOURCE (chebi, hgnc, uniprot).

Usage

pysec2pri list-versions [OPTIONS] {chebi|hgnc|uniprot}

Arguments

DATASOURCE: Required argument

ncbi

NCBI Gene mappings.

Usage

pysec2pri ncbi [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri ncbi ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

--tax-id <tax_id>

NCBI taxonomy ID.

Default:: '9606'

labels

Usage

pysec2pri ncbi labels [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | label_sec2pri | name2synonym | pri_labels | rdf | json | owl | all

--no-progress: Suppress progress bars.

--tax-id <tax_id>

NCBI taxonomy ID.

Default:: '9606'

uniprot

UniProt mappings.

Usage

pysec2pri uniprot [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri uniprot ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

--delac-file <delac_file>: Path to delac_sp.txt (UniProt).

update-ids

Resolve secondary IDs in INPUT_FILE to primary IDs using DATASOURCE.

Examples:

pysec2pri update-ids genes.tsv hgnc --at gene_id -o out.tsv
pysec2pri update-ids genes.tsv hgnc --at gene_id --synonyms label

Usage

pysec2pri update-ids [OPTIONS] INPUT_FILE {chebi|hgnc|hmdb_metabolites|hmdb_pr
                     oteins|ncbi|uniprot|wikidata}

Options

--at <COLUMN>: Required Column(s) containing IDs to resolve. Repeat for multiple.

-o, --output <output_path>: Output file (TSV or CSV).

--suffix <suffix>

New-column suffix.

Default:: '_primary'

--sep <sep>: Delimiter (inferred from extension if omitted).

--mapping <mapping_file>: Pre-built sec2pri TSV file (skips download).

--synonyms <COLUMN>: Hint column paired with –at column. Repeat to pair each.

--synonyms-mapping <synonyms_mapping_file>: Pre-built label/label mapping file for alias resolution.

--version <data_version>: Datasource release version.

--no-progress: Suppress progress bars.

Arguments

INPUT_FILE: Required argument

DATASOURCE: Required argument

update-labels

Resolve previous/alias labels in INPUT_FILE to current labels using DATASOURCE.

Examples:

pysec2pri update-labels genes.tsv hgnc --at label -o out.tsv
pysec2pri update-labels genes.tsv hgnc --at label --mapping labels.tsv

Usage

pysec2pri update-labels [OPTIONS] INPUT_FILE {chebi|hgnc|ncbi|wikidata}

Options

--at <COLUMN>: Required Column(s) containing labels to resolve. Repeat for multiple.

-o, --output <output_path>: Output file (TSV or CSV).

--suffix <suffix>

New-column suffix.

Default:: '_current'

--sep <sep>: Delimiter (inferred from extension if omitted).

--mapping <mapping_file>: Pre-built label2prev TSV file (skips download).

--synonyms <COLUMN>: Hint column paired with –at column. Repeat to pair each.

--synonyms-mapping <synonyms_mapping_file>: Pre-built mapping file for alias resolution.

--tax-id <tax_id>

NCBI taxonomy ID.

Default:: '9606'

--entity-type <entity_type>

Wikidata entity type to query. Queries all if omitted.

Options:: metabolites | chemicals | genes | proteins

--subset <subset>

Compound subset.

Default:: '3star'
Options:: 3star | complete

--version <data_version>: Datasource release version.

--no-progress: Suppress progress bars.

Arguments

INPUT_FILE: Required argument

DATASOURCE: Required argument

wikidata

wikidata mappings.

Usage

pysec2pri wikidata [OPTIONS] COMMAND [ARGS]...

ids

Usage

pysec2pri wikidata ids [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | sec2pri | pri_ids | secondary | rdf | json | owl | all

--no-progress: Suppress progress bars.

--entity-type <entity_type>

Wikidata entity type to query. Queries all if omitted.

Options:: metabolites | chemicals | genes | proteins

--test-subset: Use test SPARQL queries (LIMIT 10).

labels

Usage

pysec2pri wikidata labels [OPTIONS]

Options

--input-file <input_file>

-o, --output <output>: Output file or directory.

--version <data_version>: Datasource release version.

--format <output_format>

Output format.

Default:: 'sssom'
Options:: sssom | label_sec2pri | pri_labels | rdf | json | owl | all

--no-progress: Suppress progress bars.

--entity-type <entity_type>

Wikidata entity type to query. Queries all if omitted.

Options:: metabolites | chemicals | genes | proteins

--test-subset: Use test SPARQL queries (LIMIT 10).