Hello all, I was wondering if there was a trick to using an alignment object produced by alingment.salign() in an automodel. My current method writes the alignment to a file and then re-reads it with automodel. This is extremely clunky but based on the docs it seems the only way to go.
Current Example:
env = environ() aln = alignment(env) mdl = model(env, file = '1OPN') #The pdb model I'm using for this example. aln.append_model(mdl, align_codes = '1OPN', atom_files = '1OPN') aln.append(file = 'hiv.fasta', align_codes = 'all', alignment_format = 'fasta')
aln.salign(gap_function = True)
aln.write('tempfile.ali') #write the file
a = automodel(env, alnfile = 'tempfile.ali', sequence = 'hiv', knowns = '1OPN') #read it back in a.make()
As I expand this using the parrellel toolbox it becomes difficult to manage filenames, etc. If there was a way to just pass in the alignment object to automodel then life would be much easier.
Thanks for the help
Will