def avg_pid_by_family(fasta_filename,family):
"""
Find the .sto.pid_graph.pickle file for <family> in PID_GRAPH_DIR (there should be only one),
then calculate the average PID between all pairs of seqs in <fasta_filename>.
This is useful for calculating, say, the avg PID for Actinobacteria TPPs.
"""
pid_graph_filename = fnmatch.filter(os.listdir(PID_GRAPH_DIR),"*{0}*.sto.pid_graph.pickle".format(family))[0]
pid_graph = read_gpickle(PID_GRAPH_DIR+'/'+pid_graph_filename)
ids = []
for line in os.popen("grep \">\" {0}".format(fasta_filename)):
line = line.strip()[1:]
db_id = line[(line.rfind('_')+1):]
info = get_ncRNA_info(db_id)
ids.append(gen_accID(info['acc'],info['start'],info['end'],info['strand'],info['acc_version']))
g = pid_graph.subgraph(ids)
pids = map(lambda e: e[2],g.edges_iter())
return sum(pids)/len(pids)
def evaluate_blast_graph_count_nucleotides(graph_or_filename,hit_ratio=None,ignore_prefix=['shuffled','random']):
"""
Similar to evaluate_blast_graph, except that the real ncRNAs (in the DB, not query)
are embedded with flanking regions, and the IDs should be in
format <family>_<DB id>_<acc>/<embedded_start>-<embedded_end>
If <hit_ratio> is None, then for each node N,
sensitivity = (# of real ncRNA-neighbor nts) / (# of real ncRNA nts)
specificity = (# of real ncRNA-neighbor nts) / (# of neighbor nts)
If <hit_ratio> is defined, ex: 0.8, then for each node N,
a neighbor node M is a hit if the # of hit on M is >= <hit_ratio>*<M's ncRNA len>
NOTE: for this kind of blast output, the INPUT should be seq IDs like <family>_<db_id>
which means they are real ncRNAs with NO padding
and the DB can either be random/shuffled seqIDs
or <family>_<db_id>_<acc>/<embedded_start>-<embedded_end>
"""
rex = re.compile('(\S+)_(\d+)_(\S+)')
rex_real = re.compile('(\S+)_(\d+)')
from miscncRNA import get_ncRNA_info
if hit_ratio is not None:
hit_ratio = float(hit_ratio)
if type(graph_or_filename) is XGraph:
X = graph_or_filename
else:
X = read_gpickle(graph_or_filename)
total_nt_by_family = defaultdict(lambda: 0)
spec_by_family = defaultdict(lambda: [])
sens_by_family = defaultdict(lambda: [])
for n in X.nodes_iter():
if any(map(lambda x: n.startswith(x), ignore_prefix)): continue
if n.count('_') > 2: continue
m = rex_real.match(n)
if m is None: continue
family,query_db_id = m.group(1),m.group(2)
tmp_true = defaultdict(lambda: IntervalSet())
tmp_false = defaultdict(lambda: IntervalSet())
# the query nodes must be <family>_<db_id> (i.e. no padding)
info = get_ncRNA_info(query_db_id)
print >> sys.stderr, n
total_nt_by_family[family] += info['end']-info['start']+1
if X.degree(n) == 0: # has 0 neighbors
sens_by_family[family].append(0)
spec_by_family[family].append(0)
continue
# e is in format (local_start,local_end,score)
for (myself,neighbor,e) in X.edges_iter(n):
if any(map(lambda x: neighbor.startswith(x), ignore_prefix)):
# not a real ncRNA
tmp_false[neighbor].add(Interval(e[0],e[1]))
else:
m = rex.match(neighbor)
duncare,db_id,blob = m.group(1),m.group(2),m.group(3)
if db_id == query_db_id: continue # it's a self vs self-embedded hit, ignore
(acc,duncare),hit_start,hit_end,hit_strand = parsed_accID(blob,True,e[0],e[1])
tmp_true[db_id].add(Interval(hit_start,hit_end))
tp,fp = (0,0)
for db_id,regions in tmp_true.iteritems():
info = get_ncRNA_info(db_id)
for x in regions:
c = calc_overlap(info['start'],info['end'],x.lower_bound,x.upper_bound)
if hit_ratio is None:
tp += c
fp += (x.upper_bound-x.lower_bound+1) - c
elif c >= hit_ratio*(info['end']-info['start']+1):
tp += 1
else:
fp += 1
for some_id,regions in tmp_false.iteritems():
for x in regions: fp += x.upper_bound-x.lower_bound+1
print >> sys.stderr, tp,fp
if tp+fp == 0:
sens_by_family[family].append(0)
spec_by_family[family].append(0)
else:
sens_by_family[family].append(tp) # NOTE: it's raw count!!!
spec_by_family[family].append(tp*1./(tp+fp))
#raw_input('...')
for k in sens_by_family:
if hit_ratio is None:
sens_by_family[k] = map(lambda x: x*1./total_nt_by_family[k], sens_by_family[k])
else:
sens_by_family[k] = map(lambda x: x*1./len(total_nt_by_family[k]), sens_by_family[k])
return (None,sens_by_family,spec_by_family)
