ribolands/barmap.py
def barmap_subopts(_sname, seq, args):
    """ Print all suboptimal structures, return list of files """
    sfiles = []
    prog = ril.ProgressBar(args.stop - args.start + 1)
    for l in range(args.start, args.stop + 1):
        cseq = seq[0:l]
        cname = "{}-len_{}".format(_sname, l)

        csfile = ril.sys_suboptimals(cname, cseq,
                                     RNAsubopt=args.RNAsubopt,
                                     ener=args.s_ener,
                                     temp=args.temperature,
                                     noLP=args.noLP,
                                     sort=[
                                         '|', 'sort', '-T', args.s_sortdir, '-k3r', '-k2n'],
                                     force=args.force)
        sfiles.append(csfile)
        prog.inc()
    return sfiles
 Print all suboptimal structures, return list of files 
Print all suboptimal structures, return list of files
Print all suboptimal structures return list of files
def barmap_subopts(_sname, seq, args):
    sfiles = []
    prog = ril.ProgressBar(args.stop - args.start + 1)
    for l in range(args.start, args.stop + 1):
        cseq = seq[0:l]
        cname = "{}-len_{}".format(_sname, l)
        csfile = ril.sys_suboptimals(cname, cseq,
                                     RNAsubopt=args.RNAsubopt,
                                     ener=args.s_ener,
                                     temp=args.temperature,
                                     noLP=args.noLP,
                                     sort=[
                                         '|', 'sort', '-T', args.s_sortdir, '-k3r', '-k2n'],
                                     force=args.force)
        sfiles.append(csfile)
        prog.inc()
    return sfiles
def barmap_subopts ( _sname , seq , args ) : sfiles = [ ] prog = ril . ProgressBar ( args . stop - args . start + 1 ) for l in range ( args . start , args . stop + 1 ) : cseq = seq [ 0 : l ] cname = "{}-len_{}" . format ( _sname , l ) csfile = ril . sys_suboptimals ( cname , cseq , RNAsubopt = args . RNAsubopt , ener = args . s_ener , temp = args . temperature , noLP = args . noLP , sort = [ '|' , 'sort' , '-T' , args . s_sortdir , '-k3r' , '-k2n' ] , force = args . force ) sfiles . append ( csfile ) prog . inc ( ) return sfiles
Print all suboptimal structures, return list of files
Print all suboptimal structures return list of files
""" Print all suboptimal structures, return list of files """
_sname
seq
args