Пример #1
0
def test_get_gene_info():
    # test with HGNC symbol
    genes = list(get_gene_info(hgnc_symbols=['CHAT']))
    assert len(genes) == 1
    assert genes[0].symbol == 'CHAT'
    assert genes[0].ensembl_id == 'ENSG00000070748'

    # test with Ensembl id
    genes = list(get_gene_info(ensembl_ids=['ENSG00000156110']))
    assert len(genes) == 1
    assert genes[0].symbol == 'ADK'
    assert genes[0].ensembl_id == 'ENSG00000156110'
Пример #2
0
def test_get_gene_info():
    # test with HGNC symbol
    genes = list(get_gene_info(hgnc_symbols=['CHAT']))
    assert len(genes) == 1
    assert genes[0].symbol == 'CHAT'
    assert genes[0].ensembl_id == 'ENSG00000070748'

    # test with Ensembl id
    genes = list(get_gene_info(ensembl_ids=['ENSG00000156110']))
    assert len(genes) == 1
    assert genes[0].symbol == 'ADK'
    assert genes[0].ensembl_id == 'ENSG00000156110'
Пример #3
0
    def _get_genes(self, variant):
        """Add the genes for a variant

        Get the hgnc symbols from all transcripts and add them
        to the variant

        Args:
            variant (dict): A variant dictionary

        Returns:
            genes (list): A list of Genes
        """
        ensembl_ids = []
        hgnc_symbols = []
        
        for transcript in variant.transcripts:
            if transcript.ensembl_id:
                ensembl_ids.append(transcript.ensembl_id)
            if transcript.hgnc_symbol:
                hgnc_symbols.append(transcript.hgnc_symbol)
        
        genes = get_gene_info(
                        ensembl_ids=ensembl_ids, 
                        hgnc_symbols=hgnc_symbols
                        )
        return genes
Пример #4
0
    def _get_genes(self, variant):
        """Add the genes for a variant

            Get the hgnc symbols from all transcripts and add them
            to the variant

            Args:
                variant (dict): A variant dictionary

            Returns:
                genes (list): A list of Genes
        """
        genes = get_gene_info(variant['transcripts'])
        return genes
Пример #5
0
    def _get_genes(self, variant):
        """Add the genes for a variant

        Get the hgnc symbols from all transcripts and add them
        to the variant.

        Args:
            variant (dict): A variant dictionary

        Returns:
            genes (list): A list of Genes
        """
        transcripts = variant['transcripts']
        ensembl_ids = [transcript['ensembl_id'] for transcript in
                       transcripts if transcript['ensembl_id']]
        hgnc_symbols = [transcript['hgnc_symbol'] for transcript in
                        transcripts if transcript['hgnc_symbol']]
        genes = get_gene_info(ensembl_ids, hgnc_symbols)
        return genes
Пример #6
0
    def _get_genes(self, variant):
        """Add the genes for a variant

        Get the hgnc symbols from all transcripts and add them
        to the variant.

        Args:
            variant (dict): A variant dictionary

        Returns:
            genes (list): A list of Genes
        """
        transcripts = variant['transcripts']
        ensembl_ids = [transcript['ensembl_id'] for transcript in
                       transcripts if transcript['ensembl_id']]
        hgnc_symbols = [transcript['hgnc_symbol'] for transcript in
                        transcripts if transcript['hgnc_symbol']]
        genes = get_gene_info(ensembl_ids, hgnc_symbols)
        return genes
Пример #7
0
    def _add_genes(self, variant_obj):
        """Add the Gene objects for a variant"""
        genes = []
        ensembl_ids = []
        hgnc_symbols = []

        if variant_obj.transcripts:
            for transcript in variant_obj.transcripts:
                if transcript.ensembl_id:
                    ensembl_ids.append(transcript.ensembl_id)
                if transcript.hgnc_symbol:
                    hgnc_symbols.append(transcript.hgnc_symbol)

        else:
            hgnc_symbols = variant_obj.gene_symbols

        genes = get_gene_info(ensembl_ids=ensembl_ids, hgnc_symbols=hgnc_symbols)

        for gene in genes:
            variant_obj.add_gene(gene)
Пример #8
0
    def _add_genes(self, variant_obj):
        """Add the Gene objects for a variant"""
        genes = []
        ensembl_ids = []
        hgnc_symbols = []
        
        if variant_obj.transcripts:
            for transcript in variant_obj.transcripts:
                if transcript.ensembl_id:
                    ensembl_ids.append(transcript.ensembl_id)
                if transcript.hgnc_symbol:
                    hgnc_symbols.append(transcript.hgnc_symbol)

        else:
            hgnc_symbols = variant_obj.gene_symbols
        
        genes = get_gene_info(
                        ensembl_ids=ensembl_ids, 
                        hgnc_symbols=hgnc_symbols
                        )
            
        for gene in genes:
            variant_obj.add_gene(gene)
Пример #9
0
    def _get_genes(self, variant):
        """Add the genes for a variant

        Get the hgnc symbols from all transcripts and add them
        to the variant

        Args:
            variant (dict): A variant dictionary

        Returns:
            genes (list): A list of Genes
        """
        ensembl_ids = []
        hgnc_symbols = []

        for transcript in variant.transcripts:
            if transcript.ensembl_id:
                ensembl_ids.append(transcript.ensembl_id)
            if transcript.hgnc_symbol:
                hgnc_symbols.append(transcript.hgnc_symbol)

        genes = get_gene_info(ensembl_ids=ensembl_ids,
                              hgnc_symbols=hgnc_symbols)
        return genes