def alignmentbed2dalignedfasta(cfg):
    """
    Get sequences in FASTA format from BED file
    step#5

    :param cfg: configuration dict
    """    
    datatmpd=cfg['datatmpd']
    alignmentbedp=cfg['alignmentbedp']    
    dalignedfastap=cfg['dalignedfastap']
    logging.info(basename(dalignedfastap))
    if not exists(dalignedfastap) or cfg['force']:
        alignedfastap='{}/05_alignment.fa'.format(datatmpd)
        if not exists(alignedfastap) or cfg['force']:
            cmd=f"{cfg['bedtools']} getfasta -s -name -fi {cfg['genomep']} -bed {alignmentbedp} -fo {alignedfastap}"
            runbashcmd(cmd)

        dalignedfasta=fa2df(alignedfastap)
        dalignedfasta.columns=['aligned sequence']
        dalignedfasta=dalignedfasta.loc[(dalignedfasta.apply(lambda x: not 'N' in x['aligned sequence'],axis=1)),:] #FIXME bwa aligns to NNNNNs
        dalignedfasta.index=[i.split('(')[0] for i in dalignedfasta.index] # for bedtools 2.27, the fasta header now has hanging (+) or (-)
        dalignedfasta.index.name='id'
        dalignedfasta.to_csv(dalignedfastap,sep='\t')
    return cfg
Get sequences in FASTA format from BED file
    step#5

    :param cfg: configuration dict