datasets summary gene gene-id 1,2,3,9,10,11,12,13,14,15,16

from typing import List

from ncbi.datasets.openapi import ApiClient as DatasetsApiClient
from ncbi.datasets.openapi import ApiException as DatasetsApiException
from ncbi.datasets import GeneApi as DatasetsGeneApi
from ncbi.datasets.openapi.models import V1GeneMatch


def print_gene_information(gene_record: V1GeneMatch):
    # print query value that returned this specific gene
    print("query", gene_record.query)

    # print any errors that occured while executing the above query, e.g. invalid identifier
    if gene_record.warnings:
        print(gene_record.warnings)
    if gene_record.errors:
        print(gene_record.errors)

    # print gene metadata fields
    if gene_record.gene:
        # use returned gene structure
        print(gene_record.gene.taxname)
        # another option is to convert gene_record to python dictionary and get fields that way:
        gene_dictionary = gene_record.gene.to_dict()
        print(gene_dictionary["symbol"])


# Provide gene ids as a list of integers
gene_ids: List[int] = [2, 3, 9, 10, 11, 12, 13, 14, 15, 16]

with DatasetsApiClient() as api_client:
    gene_api = DatasetsGeneApi(api_client)
    try:
        # Retrieve gene metadata for the list of gene ids
        gene_reply = gene_api.gene_metadata_by_id(gene_ids)
        for gene in gene_reply.genes:
            print_gene_information(gene)
    except DatasetsApiException as e:
        print(f"Exception when calling GeneApi: {e}\n")

api.gene_instance <- GeneApi$new()
result_gene <- api.gene_instance$GeneMetadataById(
    '1,2,3,9,10,11,12,13,14,15,16',
    returned.content='COMPLETE',
    sort.schema.field='SORT_FIELD_GENE_ID'
)
prettify(result_gene$toJSONString())
for (gene_match in result_gene$genes)  {
    cat(gene_match$gene$gene_id, " - ", gene_match$gene$symbol, "\n")
}

datasets summary gene symbol ACRV1 A2M --taxon human

from typing import List

from ncbi.datasets.openapi import ApiClient as DatasetsApiClient
from ncbi.datasets.openapi import ApiException as DatasetsApiException
from ncbi.datasets import GeneApi as DatasetsGeneApi
from ncbi.datasets.openapi.models import V1GeneMatch


def print_gene_information(gene_record: V1GeneMatch):
    # print query value that returned this specific gene
    print("query", gene_record.query)

    # print any errors that occured while executing the above query, e.g. invalid identifier
    if gene_record.warnings:
        print(gene_record.warnings)
    if gene_record.errors:
        print(gene_record.errors)

    # print gene metadata fields
    if gene_record.gene:
        # get organism from returned gene structure
        print("organism: ", gene_record.gene.taxname)
        # another option is to convert gene_record to python dictionary and get fields that way:
        gene_dictionary = gene_record.gene.to_dict()
        # print the annotation release name, if available
        if "annotations" in gene_dictionary:
            print(gene_dictionary["annotations"][0]["release_name"])


# Provide 1 taxon - may be an NCBI taxid, scientific name or common name
taxon = "human"
# Provide gene identifiers as a list of gene symbols
gene_symbols: List[str] = ["A2M", "ACRV1"]

with DatasetsApiClient() as api_client:
    gene_api = DatasetsGeneApi(api_client)
    try:
        # For a single species retrieve gene metadata using a list of gene symbols
        gene_reply = gene_api.gene_metadata_by_tax_and_symbol(gene_symbols, taxon)
        for gene in gene_reply.genes:
            print_gene_information(gene)
    except DatasetsApiException as e:
        print(f"Exception when calling GeneApi: {e}\n")

datasets summary gene accession NM_020107.5 NP_001334352.2

from typing import List

from ncbi.datasets.openapi import ApiClient as DatasetsApiClient
from ncbi.datasets.openapi import ApiException as DatasetsApiException
from ncbi.datasets import GeneApi as DatasetsGeneApi
from ncbi.datasets.openapi.models import V1GeneMatch


def print_gene_information(gene_record: V1GeneMatch):
    # print query value that returned this specific gene
    print("query", gene_record.query)

    # print any errors that occured while executing the above query, e.g. invalid identifier
    if gene_record.warnings:
        print(gene_record.warnings)
    if gene_record.errors:
        print(gene_record.errors)

    # print gene metadata fields
    if gene_record.gene:
        # get organism from returned gene structure
        print("organism: ", gene_record.gene.taxname)
        # another option is to convert gene_record to python dictionary and get fields that way
        gene_dictionary = gene_record.gene.to_dict()
        # Print the accession and length for all transcripts
        if "transcripts" in gene_dictionary:
            for transcript in gene_dictionary["transcripts"]:
                print(
                    "transcript accession: ",
                    transcript["accession_version"],
                    "length: ",
                    transcript["length"],
                )


# Provide accessions as a list of strings
accessions: List[str] = ["NM_020107.5", "NP_001334352.2"]

with DatasetsApiClient() as api_client:
    gene_api = DatasetsGeneApi(api_client)
    try:
        # Retrieve metadata for genes with the given transcript and protein accessions
        gene_reply = gene_api.gene_metadata_by_accession(accessions)
        for gene in gene_reply.genes:
            print_gene_information(gene)
    except DatasetsApiException as e:
        print(f"Exception when calling GeneApi: {e}\n")