def __init__(self,
dbFileName, # file name to connect to
verbosity=-1 # turn off all DP chatter
):
Interface.__init__(self, dbFileName, verbosity)
self.db = TrackMDB(verbosity=verbosity)
class ViewInterface(Interface):
"""Use this interface for querying the TrackM DB"""
def __init__(self,
dbFileName, # file name to connect to
verbosity=-1 # turn off all DP chatter
):
Interface.__init__(self, dbFileName, verbosity)
self.db = TrackMDB(verbosity=verbosity)
def getOutstandingPairs(self, aniCut=95., batch=None):
"""Get all the outstanding pairs based on batch and ani cutoff
returns a list of tuples of type:
(job_id, gPath1, gPath2, gid1, gid2, batch, ani_comp)
"""
self.connect()
# get all the outstanding pairs
C = Condition("ani_comp", "=", "'-1'")
if batch is not None:
C = Condition(C, "and", Condition("batch", "=", "%s"%batch))
all_pairs = self.select('pairs', ["pid", "gid_1", "gid_2", "ani_1", "ani_2", "batch"], C)
gids = self.select('paths', ['gid', 'path'])
self.disconnect()
gids = dict(gids)
vetted_pairs = []
seen_gids = {}
for pair in all_pairs:
highest_ani = np.max([pair[3], pair[4]])
if highest_ani <= aniCut:
# pair is OK
vetted_pairs.append((pair[0], gids[pair[1]], gids[pair[2]], pair[1], pair[2], pair[5], highest_ani))
return vetted_pairs
def getGids(self):
"""Get a list of all the GIDs"""
self.connect()
gids = self.select('paths', ['gid', 'path'])
self.disconnect()
# unwrap these guys
self.gids = dict(zip([gid[0] for gid in gids], [True] * len(gids)))
return self.gids
def getGenomePaths(self):
"""Get a dict of type {gid -> path}"""
self.connect()
paths = self.select('paths', ["gid", "path"])
self.disconnect()
if len(paths) == 0:
return {}
return dict(paths)
def getContigHeaders(self):
"""Get a dict of type {'header' -> cid}"""
self.connect()
headers = self.select('contigs', ['header', 'cid'])
self.disconnect()
if len(headers) == 0:
return {}
return dict(headers)
def getHitData(self,
condition # conditional statement for searching the db
):
"""Populate a hit data instance with data that fits the given condition"""
ret_HD = HitData()
self.connect()
rows = self.select('pairs', ['pid', 'ani_comp', 'gid_1', 'gid_2'], condition=condition)
if len(rows) == 0:
return ret_HD
#print condition
#select_str = "SELECT hits.pid, len_1, len_2 FROM hits INNER JOIN pairs ON pairs.pid = hits.pid WHERE %s" % str(condition)
select_str = "SELECT hits.pid, len_1, len_2 FROM hits INNER JOIN pairs ON pairs.pid = hits.pid WHERE pairs.ani_comp <= 95 AND hits.ident >= 99 AND hits.len_1 >= 500 AND hits.len_2 >= 500"
#select_str = "SELECT hits.pid, seqs.sqid, seqs.seq FROM hits INNER JOIN seqs ON seqs.sqid = hits.sqid_1 INNER JOIN pairs ON pairs.pid = hits.pid WHERE hits.ident >= 99 AND hits.len_1 >= 500 AND hits.len_2 >= 500"
#select_str = "SELECT hits.pid, seqs.sqid, seqs.seq FROM hits INNER JOIN seqs ON seqs.sqid = hits.sqid_2 INNER JOIN pairs ON pairs.pid = hits.pid WHERE hits.ident >= 99 AND hits.len_1 >= 500 AND hits.len_2 >= 500"
print select_str
cur = self.db.getCursor()
cur.execute(select_str)
hits = cur.fetchall()
self.disconnect()
# make a tmp dict of pid -> cidTuple
pid_lookup = {}
for row in rows:
key = ret_HD.makeKey(row[2],row[3])
ret_HD.makeLookUp(row[0],key)
#pid_lookup[row[0]] = key
ret_HD.workingIds[key[0]] = False # we've seen these guys now
ret_HD.workingIds[key[1]] = False
ret_HD.addHit(key[0], key[1], 0) # cal with length 0 to initialise an empty hit between these two genomes
ret_HD.addANIIdentity(key[0], key[1], row[1]) # add the identity for this pair
"""
# now parse the seqs
for hit in hits:
seq = hit[2] # transferred sequence
sqid = hit[1]
pid = hit[0]
key = pid_lookup[hit[0]] # get the key (gid1, gid2)
print ">%s_%s" % (pid,sqid)
print seq
"""
# now parse the hits
print "No. of rows in hits data %d" % len(hits)
for hit in hits:
#print hit
length = np.mean(hit[1:]) # mean length used here
key = ret_HD.pidLookUp[hit[0]]
#key = pid_lookup[hit[0]] # get the key (gid1, gid2)
ret_HD.addHit(key[0], key[1], length) # add the length (increments hit count)
ret_HD.workingIds[key[0]] = True # we've seen these guys now
ret_HD.workingIds[key[1]] = True
return ret_HD