scout/server/blueprints/variants/controllers.py
def transcript_str(transcript_obj, gene_name=None):
    """Generate amino acid change as a string."""
    if transcript_obj.get('exon'):
        gene_part, part_count_raw = 'exon', transcript_obj['exon']
    elif transcript_obj.get('intron'):
        gene_part, part_count_raw = 'intron', transcript_obj['intron']
    else:
        # variant between genes
        gene_part, part_count_raw = 'intergenic', '0'

    part_count = part_count_raw.rpartition('/')[0]
    change_str = "{}:{}{}:{}:{}".format(
        transcript_obj.get('refseq_id', ''),
        gene_part,
        part_count,
        transcript_obj.get('coding_sequence_name', 'NA'),
        transcript_obj.get('protein_sequence_name', 'NA'),
    )
    if gene_name:
        change_str = "{}:".format(gene_name) + change_str
    return change_str
def transcript_str(transcript_obj, gene_name=None):
    if transcript_obj.get('exon'):
        gene_part, part_count_raw = 'exon', transcript_obj['exon']
    elif transcript_obj.get('intron'):
        gene_part, part_count_raw = 'intron', transcript_obj['intron']
    else:
        # variant between genes
        gene_part, part_count_raw = 'intergenic', '0'

    part_count = part_count_raw.rpartition('/')[0]
    change_str = "{}:{}{}:{}:{}".format(
        transcript_obj.get('refseq_id', ''),
        gene_part,
        part_count,
        transcript_obj.get('coding_sequence_name', 'NA'),
        transcript_obj.get('protein_sequence_name', 'NA'),
    )
    if gene_name:
        change_str = "{}:".format(gene_name) + change_str
    return change_str
def transcript_str ( transcript_obj , gene_name = None ) : if transcript_obj . get ( 'exon' ) : gene_part , part_count_raw = 'exon' , transcript_obj [ 'exon' ] elif transcript_obj . get ( 'intron' ) : gene_part , part_count_raw = 'intron' , transcript_obj [ 'intron' ] else : # variant between genes gene_part , part_count_raw = 'intergenic' , '0' part_count = part_count_raw . rpartition ( '/' ) [ 0 ] change_str = "{}:{}{}:{}:{}" . format ( transcript_obj . get ( 'refseq_id' , '' ) , gene_part , part_count , transcript_obj . get ( 'coding_sequence_name' , 'NA' ) , transcript_obj . get ( 'protein_sequence_name' , 'NA' ) , ) if gene_name : change_str = "{}:" . format ( gene_name ) + change_str return change_str
Generate amino acid change as a string.
Generate amino acid change as a string .