def adjust_scores(dataset_name, *batchscore_ids, **kwargs):
"""
Create normalized versions of batchscore runs in `batchscore_ids`.
Note that zscores with an absolute of higher than 5 are chopped off (set to 5).
"""
if 'overwrite' in kwargs:
overwrite = kwargs['overwrite']
else:
overwrite = False
# Determine adjustment type
adj_type = None
for k,v in kwargs.iteritems():
if k in ['norm', 'window', 'neg']:
if adj_type:
raise Exception("Cannot adjust in multiple ways: %s, %s" % (adj_type, k))
if k == 'window':
window_size = int(v)
adj_type = '%s_%d' % (k, window_size)
else:
adj_type = k
# Perform adjustments on all scores..
for batchscore_id in batchscore_ids:
dc = DATASET_CONFIGS[dataset_name]
ds_dir = get_batchscore_dir(dataset_name)
sc_dir = os.path.join(ds_dir, batchscore_id)
sc_dir_adj = "%s-%s" % (sc_dir, adj_type)
if not overwrite:
resp = raw_input("Creating %s'd version of\n %s\nat\n %s\nContinue? y/[n]: "
% (adj_type, sc_dir, sc_dir_adj))
if resp != 'y':
continue
if not os.path.exists(sc_dir_adj):
os.mkdir(sc_dir_adj)
else:
for fname in os.listdir(sc_dir_adj):
os.remove(os.path.join(sc_dir_adj, fname))
align_files = dc.get_align_files()
for align_file in align_files:
out_file = dc.get_out_file(align_file, sc_dir)
if not os.path.exists(out_file):
continue
scores = read_batchscores(out_file)
if adj_type is 'norm':
scores_adj = norm_scores(scores, filter=5)
elif adj_type is 'neg':
scores_adj = [-s for s in scores]
elif adj_type.startswith('window'):
scores_adj = window_scores(scores, window_size)
out_file_adj = os.path.join(sc_dir_adj, os.path.split(out_file)[-1])
write_batchscores(out_file_adj, scores_adj)
print "Created %s" % sc_dir_adj
def run_experiment(align_file):
"""
Run scorers on one aln file. This is a helper for multithreading the
scoring of each aln file.
"""
alignment = Alignment(align_file)
for scorer in scorers:
# Score.
try:
scores = scorer.score(alignment)
except Exception, e:
import traceback
sys.stderr.write("\nError scoring %s via %s\n" %
(alignment.align_file, type(scorer).__name__))
traceback.print_exc()
continue
# Write scores.
out_file = dataset_config.get_out_file(align_file, scorer.output_dir)
write_batchscores(out_file, scores)
