scout/commands/convert.py
def convert(context, panel):
    """Convert a gene panel with hgnc symbols to a new one with hgnc ids."""
    adapter = context.obj['adapter']
    new_header = ["hgnc_id","hgnc_symbol","disease_associated_transcripts",
                 "reduced_penetrance", "genetic_disease_models", "mosaicism",
                 "database_entry_version"]
    
    genes = parse_genes(panel)
    
    adapter.add_hgnc_id(genes)
    
    click.echo("#{0}".format('\t'.join(new_header)))
    for gene in genes:
        if gene.get('hgnc_id'):
            print_info = []
            for head in new_header:
                print_info.append(str(gene[head]) if gene.get(head) else '')
            
            click.echo('\t'.join(print_info))
def convert(context, panel):
    """Convert a gene panel with hgnc symbols to a new one with hgnc ids."""
    adapter = context.obj['adapter']
    new_header = ["hgnc_id","hgnc_symbol","disease_associated_transcripts",
                 "reduced_penetrance", "genetic_disease_models", "mosaicism",
                 "database_entry_version"]
    
    genes = parse_genes(panel)
    
    adapter.add_hgnc_id(genes)
    
    click.echo("#{0}".format('\t'.join(new_header)))
    for gene in genes:
        if gene.get('hgnc_id'):
            print_info = []
            for head in new_header:
                print_info.append(str(gene[head]) if gene.get(head) else '')
            
            click.echo('\t'.join(print_info))
def convert ( context , panel ) : adapter = context . obj [ 'adapter' ] new_header = [ "hgnc_id" , "hgnc_symbol" , "disease_associated_transcripts" , "reduced_penetrance" , "genetic_disease_models" , "mosaicism" , "database_entry_version" ] genes = parse_genes ( panel ) adapter . add_hgnc_id ( genes ) click . echo ( "#{0}" . format ( '\t' . join ( new_header ) ) ) for gene in genes : if gene . get ( 'hgnc_id' ) : print_info = [ ] for head in new_header : print_info . append ( str ( gene [ head ] ) if gene . get ( head ) else '' ) click . echo ( '\t' . join ( print_info ) )
Convert a gene panel with hgnc symbols to a new one with hgnc ids.
Convert a gene panel with hgnc symbols to a new one with hgnc ids .