def setAlignments( seqs = None, profiles = None, run_id = None, ali_type = 'struct',
**kwargs ):
'''
Make N structural alignemnts for each of N profiles
having the same M sequences apiece.
'''
assert seqs; assert run_id; assert profiles
ns = len(profiles)
nq = len(seqs)
rutils = utils
if ali_type == 'struct':
ali_out = [infernal.alignment(seqs, p, run_id) for p in profiles]
alignments = [a[0] for a in ali_out]
refs = [[a[1]]*nq for a in ali_out]
stks = [a[2] for a in ali_out]
pairs = [[rutils.stk_pairs(stk)]*nq for stk in stks]
elif ali_type == 'muscle':
alignment = muscle.align(seqs)
alignments = [alignment] * ns
refs = None
pairs = None
stks = None
#raise Exception('MUSCLE ALIGNMENT NOT YET IMPLEMENTED... SORRY :(')
#ONCE IMPLEMENTED, WILL FIND HOMOLOGOUS STRUCTURES FOR EACH
#PROFILE IN THE GIVEN MULTIPLE SEQUENCE ALIGNMENT.
#IT REMAINS UNCLEAR HOW I WILL PUT THESE INTO A TREE AND TRACK THE
#STRUCTURAL ELEMENTS THROUGH IT!
#all_refs = []
#all_pairs = []
#for i, profile in enumerate(profiles):
# these_refs = []
# these_pairs = []
# for j, q in enumerate(seqs):
# ali_out = [infernal.alignment([q],profile, run_id)]
# these_refs.append(ali_out[0][1])
# stk = ali_out[0][2]
#
# this_ali = ali_out[0][0]
# this_seq = this_ali[0]
# all_seqs.append(this_seq)
# these_pairs.append( rutils.stk_pairs(stk))
# raise Exception()
# all_refs.append(these_refs)
# all_pairs.append(these_pairs)
refs = None
pairs = None
else:
raise Exception('sorry not implemented')
return alignments, refs, pairs
def align_seqnodes(recs,**kwargs): align = muscle.align(recs) return align
