scout/commands/export/transcript.py
def transcripts(context, build):
    """Export all transcripts to .bed like format"""
    LOG.info("Running scout export transcripts")
    adapter = context.obj['adapter']
    
    header = ["#Chrom\tStart\tEnd\tTranscript\tRefSeq\tHgncID"]

    for line in header:
        click.echo(line)

    transcript_string = ("{0}\t{1}\t{2}\t{3}\t{4}\t{5}")

    for tx_obj in export_transcripts(adapter):
        click.echo(transcript_string.format(
            tx_obj['chrom'],
            tx_obj['start'],
            tx_obj['end'],
            tx_obj['ensembl_transcript_id'],
            tx_obj.get('refseq_id',''),
            tx_obj['hgnc_id'],
            )
        )
def transcripts(context, build):
    LOG.info("Running scout export transcripts")
    adapter = context.obj['adapter']
    
    header = ["#Chrom\tStart\tEnd\tTranscript\tRefSeq\tHgncID"]

    for line in header:
        click.echo(line)

    transcript_string = ("{0}\t{1}\t{2}\t{3}\t{4}\t{5}")

    for tx_obj in export_transcripts(adapter):
        click.echo(transcript_string.format(
            tx_obj['chrom'],
            tx_obj['start'],
            tx_obj['end'],
            tx_obj['ensembl_transcript_id'],
            tx_obj.get('refseq_id',''),
            tx_obj['hgnc_id'],
            )
        )
def transcripts ( context , build ) : LOG . info ( "Running scout export transcripts" ) adapter = context . obj [ 'adapter' ] header = [ "#Chrom\tStart\tEnd\tTranscript\tRefSeq\tHgncID" ] for line in header : click . echo ( line ) transcript_string = ( "{0}\t{1}\t{2}\t{3}\t{4}\t{5}" ) for tx_obj in export_transcripts ( adapter ) : click . echo ( transcript_string . format ( tx_obj [ 'chrom' ] , tx_obj [ 'start' ] , tx_obj [ 'end' ] , tx_obj [ 'ensembl_transcript_id' ] , tx_obj . get ( 'refseq_id' , '' ) , tx_obj [ 'hgnc_id' ] , ) )
Export all transcripts to .bed like format
Export all transcripts to . bed like format