"""
tha:ACCL02000010.1/116901-116991
hak:ACKX01000080.1/10519-10620
?hac:ACCL02000010.1/116901-116991 # this is redundant
haq:AAQK01002704.1/947-1059
hcp:CP001034.1/2651359-2651454
"""
#ids = ['ACCL02000010.1/116901-116991', '4lvv', 'ACKX01000080.1/10519-10620',
from rna_pdb_tools.utils.rna_alignment.rna_alignment import RNAalignment

haq = "UGCAAAAUAGGUUUCCAUGCGUCAAGUGUUUUGUGGAUGGGGAGUUGCCACAGAAACGAAAAGUCGGUUCGCGUGCGGACCGGACUUACGAUAUGGUUACCGCACCCGUUGCA"
a = RNAalignment('RF01831.stockholm_r85p.sto')
a.find_seq_in_align(haq)
hac = "AGUAGAGUAGGUCUUAUACGUAAAGUGUCAUCGGAUGGGGAGACUUCCGGUGAACGAAGGGUUACCGCGUUAUAUGACCGCUUCCGCUACU"
a.find_seq_in_align(hac)

ids = ['ACCL02000010.1/116901-116991', 
          'ACKX01000080.1/10519-10620',
          'AAQK01002704.1/947-1059',
          'CP001034.1/2651359-2651454',
           '4lVV']

sub =  a.subset(ids)
sub.write('sub.sto')