def get_loci_fasta(loci, out_fa, ref):
    """get fasta from precursor"""
    if not find_cmd("bedtools"):
        raise ValueError("Not bedtools installed")
    with make_temp_directory() as temp:
        bed_file = os.path.join(temp, "file.bed")
        for nc, loci in loci.iteritems():
            for l in loci:
                with open(bed_file, 'w') as bed_handle:
                    logger.debug("get_fasta: loci %s" % l)
                    nc, c, s, e, st = l
                    print("{0}\t{1}\t{2}\t{3}\t{3}\t{4}".format(c, s, e, nc, st), file=bed_handle)
                get_fasta(bed_file, ref, out_fa)
    return out_fa
def get_loci_fasta ( loci , out_fa , ref ) : if not find_cmd ( "bedtools" ) : raise ValueError ( "Not bedtools installed" ) with make_temp_directory ( ) as temp : bed_file = os . path . join ( temp , "file.bed" ) for nc , loci in loci . iteritems ( ) : for l in loci : with open ( bed_file , 'w' ) as bed_handle : logger . debug ( "get_fasta: loci %s" % l ) nc , c , s , e , st = l print ( "{0}\t{1}\t{2}\t{3}\t{3}\t{4}" . format ( c , s , e , nc , st ) , file = bed_handle ) get_fasta ( bed_file , ref , out_fa ) return out_fa
get fasta from precursor