scout/server/blueprints/variants/controllers.py
def variant_export_lines(store, case_obj, variants_query):
    """Get variants info to be exported to file, one list (line) per variant.

        Args:
            store(scout.adapter.MongoAdapter)
            case_obj(scout.models.Case)
            variants_query: a list of variant objects, each one is a dictionary

        Returns:
            export_variants: a list of strings. Each string  of the list corresponding to the fields
                             of a variant to be exported to file, separated by comma
    """

    export_variants = []

    for variant in variants_query:
        variant_line = []
        position = variant['position']
        change = variant['reference']+'>'+variant['alternative']
        variant_line.append(variant['rank_score'])
        variant_line.append(variant['chromosome'])
        variant_line.append(position)
        variant_line.append(change)
        variant_line.append('_'.join([str(position), change]))

        # gather gene info:
        gene_list = variant.get('genes') #this is a list of gene objects
        gene_ids = []
        gene_names = []
        hgvs_c = []

        # if variant is in genes
        if len(gene_list) > 0:
            for gene_obj in gene_list:
                hgnc_id = gene_obj['hgnc_id']
                gene_name = gene(store, hgnc_id)['symbol']

                gene_ids.append(hgnc_id)
                gene_names.append(gene_name)

                hgvs_nucleotide = '-'
                # gather HGVS info from gene transcripts
                transcripts_list = gene_obj.get('transcripts')
                for transcript_obj in transcripts_list:
                    if transcript_obj.get('is_canonical') and transcript_obj.get('is_canonical') is True:
                        hgvs_nucleotide = str(transcript_obj.get('coding_sequence_name'))
                hgvs_c.append(hgvs_nucleotide)

            variant_line.append(';'.join( str(x) for x in  gene_ids))
            variant_line.append(';'.join( str(x) for x in  gene_names))
            variant_line.append(';'.join( str(x) for x in  hgvs_c))
        else:
            while i < 4:
                variant_line.append('-') # instead of gene ids
                i = i+1

        variant_gts = variant['samples'] # list of coverage and gt calls for case samples
        for individual in case_obj['individuals']:
            for variant_gt in variant_gts:
                if individual['individual_id'] == variant_gt['sample_id']:
                    # gather coverage info
                    variant_line.append(variant_gt['allele_depths'][0]) # AD reference
                    variant_line.append(variant_gt['allele_depths'][1]) # AD alternate
                    # gather genotype quality info
                    variant_line.append(variant_gt['genotype_quality'])

        variant_line = [str(i) for i in variant_line]
        export_variants.append(",".join(variant_line))

    return export_variants
def variant_export_lines(store, case_obj, variants_query):
    """Get variants info to be exported to file, one list (line) per variant.

        Args:
            store(scout.adapter.MongoAdapter)
            case_obj(scout.models.Case)
            variants_query: a list of variant objects, each one is a dictionary

        Returns:
            export_variants: a list of strings. Each string  of the list corresponding to the fields
                             of a variant to be exported to file, separated by comma
    """

    export_variants = []

    for variant in variants_query:
        variant_line = []
        position = variant['position']
        change = variant['reference']+'>'+variant['alternative']
        variant_line.append(variant['rank_score'])
        variant_line.append(variant['chromosome'])
        variant_line.append(position)
        variant_line.append(change)
        variant_line.append('_'.join([str(position), change]))

        # gather gene info:
        gene_list = variant.get('genes') #this is a list of gene objects
        gene_ids = []
        gene_names = []
        hgvs_c = []

        # if variant is in genes
        if len(gene_list) > 0:
            for gene_obj in gene_list:
                hgnc_id = gene_obj['hgnc_id']
                gene_name = gene(store, hgnc_id)['symbol']

                gene_ids.append(hgnc_id)
                gene_names.append(gene_name)

                hgvs_nucleotide = '-'
                # gather HGVS info from gene transcripts
                transcripts_list = gene_obj.get('transcripts')
                for transcript_obj in transcripts_list:
                    if transcript_obj.get('is_canonical') and transcript_obj.get('is_canonical') is True:
                        hgvs_nucleotide = str(transcript_obj.get('coding_sequence_name'))
                hgvs_c.append(hgvs_nucleotide)

            variant_line.append(';'.join( str(x) for x in  gene_ids))
            variant_line.append(';'.join( str(x) for x in  gene_names))
            variant_line.append(';'.join( str(x) for x in  hgvs_c))
        else:
            while i < 4:
                variant_line.append('-') # instead of gene ids
                i = i+1

        variant_gts = variant['samples'] # list of coverage and gt calls for case samples
        for individual in case_obj['individuals']:
            for variant_gt in variant_gts:
                if individual['individual_id'] == variant_gt['sample_id']:
                    # gather coverage info
                    variant_line.append(variant_gt['allele_depths'][0]) # AD reference
                    variant_line.append(variant_gt['allele_depths'][1]) # AD alternate
                    # gather genotype quality info
                    variant_line.append(variant_gt['genotype_quality'])

        variant_line = [str(i) for i in variant_line]
        export_variants.append(",".join(variant_line))

    return export_variants
Get variants info to be exported to file, one list (line) per variant.

        Args:
            store(scout.adapter.MongoAdapter)
            case_obj(scout.models.Case)
            variants_query: a list of variant objects, each one is a dictionary

        Returns:
            export_variants: a list of strings. Each string  of the list corresponding to the fields
                             of a variant to be exported to file, separated by comma