scout/export/variant.py
def export_mt_variants(variants, sample_id):
    """Export mitochondrial variants for a case to create a MT excel report

    Args:
        variants(list): all MT variants for a case, sorted by position
        sample_id(str) : the id of a sample within the case

    Returns:
        document_lines(list): list of lines to include in the document
    """
    document_lines = []
    for variant in variants:
        line = []
        position = variant.get('position')
        change = '>'.join([variant.get('reference'),variant.get('alternative')])
        line.append(position)
        line.append(change)
        line.append(str(position)+change)
        genes = []
        prot_effect = []
        for gene in variant.get('genes'):
            genes.append(gene.get('hgnc_symbol',''))
            for transcript in gene.get('transcripts'):
                if transcript.get('is_canonical') and transcript.get('protein_sequence_name'):
                    prot_effect.append(urllib.parse.unquote(transcript.get('protein_sequence_name')))
        line.append(','.join(prot_effect))
        line.append(','.join(genes))
        ref_ad = ''
        alt_ad = ''
        for sample in variant['samples']:
            if sample.get('sample_id') == sample_id:
                ref_ad = sample['allele_depths'][0]
                alt_ad = sample['allele_depths'][1]
        line.append(ref_ad)
        line.append(alt_ad)
        document_lines.append(line)
    return document_lines
def export_mt_variants(variants, sample_id):
    document_lines = []
    for variant in variants:
        line = []
        position = variant.get('position')
        change = '>'.join([variant.get('reference'),variant.get('alternative')])
        line.append(position)
        line.append(change)
        line.append(str(position)+change)
        genes = []
        prot_effect = []
        for gene in variant.get('genes'):
            genes.append(gene.get('hgnc_symbol',''))
            for transcript in gene.get('transcripts'):
                if transcript.get('is_canonical') and transcript.get('protein_sequence_name'):
                    prot_effect.append(urllib.parse.unquote(transcript.get('protein_sequence_name')))
        line.append(','.join(prot_effect))
        line.append(','.join(genes))
        ref_ad = ''
        alt_ad = ''
        for sample in variant['samples']:
            if sample.get('sample_id') == sample_id:
                ref_ad = sample['allele_depths'][0]
                alt_ad = sample['allele_depths'][1]
        line.append(ref_ad)
        line.append(alt_ad)
        document_lines.append(line)
    return document_lines
def export_mt_variants ( variants , sample_id ) : document_lines = [ ] for variant in variants : line = [ ] position = variant . get ( 'position' ) change = '>' . join ( [ variant . get ( 'reference' ) , variant . get ( 'alternative' ) ] ) line . append ( position ) line . append ( change ) line . append ( str ( position ) + change ) genes = [ ] prot_effect = [ ] for gene in variant . get ( 'genes' ) : genes . append ( gene . get ( 'hgnc_symbol' , '' ) ) for transcript in gene . get ( 'transcripts' ) : if transcript . get ( 'is_canonical' ) and transcript . get ( 'protein_sequence_name' ) : prot_effect . append ( urllib . parse . unquote ( transcript . get ( 'protein_sequence_name' ) ) ) line . append ( ',' . join ( prot_effect ) ) line . append ( ',' . join ( genes ) ) ref_ad = '' alt_ad = '' for sample in variant [ 'samples' ] : if sample . get ( 'sample_id' ) == sample_id : ref_ad = sample [ 'allele_depths' ] [ 0 ] alt_ad = sample [ 'allele_depths' ] [ 1 ] line . append ( ref_ad ) line . append ( alt_ad ) document_lines . append ( line ) return document_lines
Export mitochondrial variants for a case to create a MT excel report

    Args:
        variants(list): all MT variants for a case, sorted by position
        sample_id(str) : the id of a sample within the case

    Returns:
        document_lines(list): list of lines to include in the document
Export mitochondrial variants for a case to create a MT excel report