for dir in dirs:
print "Working on %s\n" % dir
aligned_files = glob.glob('%sFC_*/hmmalign.results.*' % dir)
sequence_files = glob.glob('%sFC_*/hmmalign.frag.*' % dir)
base_alignment_file = glob.glob('%s/*.fasta' % dir)
base_alignment = MutableAlignment()
done = base_alignment.read_filepath(base_alignment_file[0])
subbackbone = original_backbone.get_soft_sub_alignment(base_alignment.get_sequence_names())
frags = MutableAlignment()
sequence_names = []
for file in sequence_files:
seq = MutableAlignment()
done = seq.read_filepath(file)
done = sequence_names.extend(seq.get_sequence_names())
for name, seq in seq.iteritems():
frags[name] = seq.upper()
problem = SeppProblem(sequence_names)
problem.set_subalignment(subbackbone)
mut_subalg = problem.subalignment.get_mutable_alignment()
remaining_cols = mut_subalg.delete_all_gap()
problem.annotations["ref.alignment.columns"] = remaining_cols
problem.fragments = frags
ap_alg = problem.read_extendend_alignment_and_relabel_columns\
(base_alignment_file, aligned_files)
extendedAlignment.merge_in(ap_alg,convert_to_string=False)
extendedAlignment.write_to_path("/projects/sate8/namphuon/ultra_large/1000000/upp_100_10_new/upp.unmasked.fasta")
extendedAlignment.remove_insertion_columns()
extendedAlignment.write_to_path("/projects/sate8/namphuon/ultra_large/1000000/upp_100_10_new/upp.masked.fasta")
