def eval_original_fna(fasta_filename):
"""
Reads a fasta file and returns (ncRNA family, # of seqs belonging to the family, clique size)
ncRNA family is determined by plurality, which can be None.
"""
tally_by_family = defaultdict(lambda: 0)
ids_hit_by_family = defaultdict(lambda: set())
clique_size = 0
for id in os.popen("grep \"^>\" " + fasta_filename):
id = id.strip()[1:]
clique_size += 1
#id = id[:id.rfind('_')] # what was this for???
(acc,junk),strand,start,end = parsed_accID(id,True)
ncRNA_id, ncRNA_family = get_ribo1(acc,start,end)
tally_by_family[ncRNA_family] += 1
ids_hit_by_family[ncRNA_family].add( ncRNA_id )
tally_by_family = tally_by_family.items()
tally_by_family.sort(key=itemgetter(1))
fam,count = tally_by_family[-1]
# HACK HERE!!!
if fam is None and len(tally_by_family) > 1:
if tally_by_family[-2][1] >= 0.5*clique_size:
lesser_fam = tally_by_family[-2][0] + '-'
return lesser_fam,tally_by_family[-2][1],clique_size,ids_hit_by_family[tally_by_family[-2][0]]
elif tally_by_family[-2][1] >= 3:
lesser_fam = tally_by_family[-2][0] + '--'
return lesser_fam,tally_by_family[-2][1],clique_size,ids_hit_by_family[tally_by_family[-2][0]]
return fam,count,clique_size,ids_hit_by_family[fam]
def eval_clique(Q, cursor):
"""
Given Q which is a clique containing node indices, look it up
on the db using cursor.
Like eval_original_fna, returns:
(fam, # of seqs belonging to fam, clique_size, fam ids hit)
"""
FETCH_SQL = "SELECT n.id,s.start,s.end \
FROM sets_for_nodes s \
LEFT JOIN nodes_to_index AS n \
ON (s.nodes_ind=n.ind) WHERE i={i}"
T = defaultdict(lambda: 0) # fam ---> hit count
H = defaultdict(lambda: set()) # fam ---> set of ids hit
for i in Q:
cursor.execute( FETCH_SQL.format(i=i) )
_id,_loc_start,_loc_end = cursor.fetchone()
(acc,junk),strand,start,end = parsed_accID(_id, True, _loc_start, _loc_end)
id, fam = get_ribo1( acc, start, end )
T[fam] += 1
H[fam].add( id )
T = T.items()
T.sort(key=itemgetter(1), reverse=True)
fam,count = T[0]
# HACK
if fam is None and len(T)>1:
if T[1][1] >= 0.5*len(Q):
return T[1][0]+'-',T[1][1],len(Q),H[T[1][0]]
elif T[1][1] >= 3:
return T[1][0]+'--',T[1][1],len(Q),H[T[1][0]]
return fam, count, len(Q), H[fam]
def read_cmfinder_motif(motif_filename):
"""
Reads a motif file (outputted by CMfinder, stockholm format)
Returns (ncRNA family, # of motif members belonging to the family, # of motif members)
ncRNA family is determined by plurality. family is None if plurality are not ncRNAs.
"""
tally_by_family = defaultdict(lambda: 0)
motif_size = 0
with open(motif_filename) as f:
f.readline()
f.readline()
for line in f:
if len(line.strip()) == 0:
continue
feature, text, annot = line.strip().split(None,2)
if feature == '#=GS' and annot.startswith('DE'):
break
if feature == '#=GS' and annot.startswith('WT'):
motif_size += 1
print >> sys.stderr, "looking up id", text
#id = id[:id.rfind('_')] # what was this for?
(acc,junk),strand,start,end = parsed_accID(text,True)
ncRNA_id, ncRNA_family = get_ribo1(acc,start,end)
tally_by_family[ncRNA_family] += 1
print >> sys.stderr, "motif filename is", motif_filename
print >> sys.stderr, "tally by family is", tally_by_family
tally_by_family = tally_by_family.items()
tally_by_family.sort(key=itemgetter(1))
fam,count = tally_by_family[-1]
return fam,count,motif_size
def check_hit(i, cursor=None):
"""
Given <i>, piece up its accession #, start, end,
and call get_ribo1 which will return (<ncRNA_id>,<ncRNA_family>)
if it is a hit or (None,None) if not a hit
"""
from miscRibo import get_ribo1
del_it = False
if cursor is None:
conn = CONN_FUNC()
cursor = get_dict_cursor(conn)
del_it = True
cursor.execute("SELECT n.id,s.start,s.end \
FROM sets_for_nodes AS s \
LEFT JOIN nodes_to_index AS n \
ON (s.nodes_ind=n.ind) WHERE i={0}".format(i))
r = cursor.fetchone()
(acc,junk),strand,start,end = parsed_accID(r['id'],True,r['start'],r['end'])
if del_it:
conn.close()
return get_ribo1(acc,start,end)
