def h_analysis(htrees, seq_diff, regions, mhcs_dict):
a = NGclassify.Classify()
#print "Classification of sequence %s" % seq_diff.obj.name
for htree, name in htrees:
print "Classification according to tree:", name
a.classify_by_tree(htree, seq_diff, regions)
#print "start is ", seq_diff.start
#print "end is ", seq_diff.end
#print "haplo_stats: ", a.haplo_stats
print "genome_state is ", a.get_genome_state()
(haplo_stats_sorted, haplo_best) = a.prediction_sorting()
print haplo_best
#print "haplo_stats_sorted is:\n", haplo_stats_sorted
print "=" * 20
#print "haplo_best is: ", haplo_best
#print "finding MHCS for sequence %s" % seq_diff.obj.name
mhcss = a.get_mhcss(mhcs_dict)
#print "MHCS ID for sequence %s is %s" % (seq_diff.obj.name, ','.join(list(mhcss)))
# PROVA PRINT
# print "stat_list is:"
# print type(a.__dict__['stat_list'])
#print a.__dict__
print '-' * 30
#print a.seq_diff.obj.name
#print a.haplo_stats
#pdb.set_trace()
return a
def align_sequence(muscle_exe, sequence, rif=None, ):
"""sequence is a datatypes.Sequence, rif"""
if rif is None:
rif = datatypes.Sequence('RSRS', consts.RCRS)
seq_diff = NGclassify.SequenceDiff()
#print "Aligning sequence %s" % sequence.name
seq_diff.gen_diff(muscle_exe, rif, datatypes.Sequence(sequence.name, str(sequence)))
#print "-"*30
return seq_diff
def h_analysis(htrees, seq_diff, regions, mhcs_dict):
a = NGclassify.Classify()
#print "Classification of sequence %s" % seq_diff.obj.name
for htree, name in htrees:
print "Classification according to tree:", name
a.classify_by_tree(htree, seq_diff, regions)
#print "start is ", seq_diff.start
#print "end is ", seq_diff.end
#print "haplo_stats: ", a.haplo_stats
print "genome_state is ", a.get_genome_state()
(haplo_stats_sorted, haplo_best) = a.prediction_sorting()
print haplo_best
#print "haplo_stats_sorted is:\n", haplo_stats_sorted
print "="*20
mhcss = a.get_mhcss(mhcs_dict)
print '-'*30
return a