def get_pacbps_by_nodes(self, node1=None, node2=None, order_by='bits'):
"""
Get the pacbp(s) from the CodingBlockGraph by node, optional two nodes
@type node1: *
@param node1: node identifier
@type node2: *
@param node2: node identifier (or None)
@type order_by: string
@param order_by: 'length' (DESC), 'bits' (DESC), 'start' (ASC);
default 'bits'
@rtype: list
@return: list of pacbps objects
@attention: when only a single node is requested, pacbp(s) are swapped
to make the requested node the query node
"""
if node1 not in self.get_nodes():
message = "node1 `%s` not in graph: %s" % (node1, self.get_nodes())
raise InproperlyAppliedArgument, message
if node2 and node2 not in self.get_nodes():
message = "node2 `%s` not in graph: %s" % (node2, self.get_nodes())
raise InproperlyAppliedArgument, message
if order_by not in ['bits', 'length']:
order_by = 'bits'
# if no pacbps are stored into the object yet, return []
if not self.pacbps: return []
thepacbps = []
for (key, nodeA, nodeB), pacbporf in self.pacbps.iteritems():
if nodeA == node1 or nodeB == node1:
if not node2:
if nodeA == node1:
thepacbps.append(pacbporf)
else:
# swap query and sbjct!
thispacbporf = pacb.swap_query_and_sbjct(pacbporf)
thepacbps.append(thispacbporf)
else:
if nodeA == node2 or nodeB == node2:
thepacbps.append(pacbporf)
else:
pass
# order the requested pacbps
if order_by == 'bits':
thepacbps = ordering.order_list_by_attribute(thepacbps,
"bits",
reversed=True)
else:
thepacbps = ordering.order_list_by_attribute(thepacbps,
"length",
reversed=True)
# return the requested pacbps
return thepacbps
def hmmresults2splittedpacbps(results,hmmcoords,target,informant,inwpCBG,input,gapsize=2,min_bitscore=0):
""" """
hmm_pacbporf_list = []
for hmmhit in results:
( sbjct_header, sbjct_start, sbjct_end, query_start, query_end,
query, match, sbjct, score, expect ) = hmmhit
if score < min_bitscore: continue
_org,orfid = hmmhit[0].split('_orf_')
orfSbjct = input[informant]['orfs'].get_orf_by_id( int(orfid) )
orfQuery = inwpCBG.get_orfs_of_graph(target)[0]
querycoords = ( min(hmmcoords[target]),max(hmmcoords[target]) )
key_data, hmmpacbporf = hmmhit2pacbp(
orfQuery,target,querycoords,
orfSbjct,informant,hmmhit)
# check if hmmpacbporf creation was succesfull
if not hmmpacbporf: continue
# if here, unextend and split on gapsize
(pacbpkey,qNode,sNode) = key_data
hmmpacbporf.unextend_pacbporf()
splittedhmmpacbporfs, splittedstatus =\
split_pacb_on_gaps(hmmpacbporf,gapsize=gapsize)
# loop over the splitted ones and store high(er) scoring fractions
for splittedhmmpf in splittedhmmpacbporfs:
# added code to strip unmatched ends. Should not
# be neccesarily anymore, but just to be certain
# no leading/trailing gaps are there
# if '-' in [ splittedhmmpf.query[0], splittedhmmpf.sbjct[0],
# splittedhmmpf.query[-1], splittedhmmpf.sbjct[-1] ]:
# hmmpacbp = pacbporf2pacbp(splittedhmmpf)
# hmmpacbp.strip_unmatched_ends()
# if not hmmpacbp: continue
# if len(hmmpacbp) <= 1: continue
# # if here, make again a pacbporf of the pacbp
# splittedhmmpf = pacbp2pacbporf(hmmpacbp,splittedhmmpf.orfQ,splittedhmmpf.orfS)
if splittedhmmpf.bitscore < min_bitscore: continue
# check if query/sbjct must be swapped
queryNode = (target,orfQuery.id)
sbjctNode = (informant,orfSbjct.id)
if qNode == queryNode:
pass
elif qNode == sbjctNode:
# swap query and sbjct!
splittedhmmpf = swap_query_and_sbjct(splittedhmmpf)
else:
# whaaaat else !?
raise "UNEXPECTED EVENT"
# append to hmm_pacbporf_list
hmm_pacbporf_list.append( splittedhmmpf )
# return bitscore ordered list of hmmpacbporfs
return _order_list_by_attribute(hmm_pacbporf_list,
order_by='bitscore',reversed=True)
def get_pacbps_by_organism(self, organism, order_by=None):
"""
Get the pacbp(s) from the CodingBlockGraph of a single organism
@type organism: * (string)
@param organism: Organism identifier
@type order_by: string
@param order_by: 'length' (DESC), 'bits' (DESC), 'node' or None
(on node); default None
@rtype: list
@return: list of pacbps objects
@attention: pacbps are swapped such that `organism` is always the query!
@attention: pacbps are ordered by their sbjct nodes
"""
# check if requested organism is present in this graph
if organism not in self.organism_set():
raise OrganismNotPresentInGraph
# if no pacbps are stored into the object yet, return []
if not self.pacbps: return []
# reset order_by if falsely assigned
if order_by not in [None, 'bits', 'length']:
order_by = None
thepacbps = []
for (key, (org1, orf1), (org2,
orf2)), pacbporf in self.pacbps.iteritems():
if organism == org1:
thepacbps.append(((org2, orf2), pacbporf))
elif organism == org2:
# swap query and sbjct!
thispacbporf = pacb.swap_query_and_sbjct(pacbporf)
thepacbps.append(((org1, orf1), thispacbporf))
else:
pass
# sort the requested pacbps on Node
thepacbps.sort()
thepacbps = [pacbporf for node, pacbporf in thepacbps]
# order the requested pacbps if requested for
if order_by == 'bits':
thepacbps = ordering.order_list_by_attribute(thepacbps,
"bits",
reversed=True)
if order_by == 'length':
thepacbps = ordering.order_list_by_attribute(thepacbps,
"length",
reversed=True)
# return the requested pacbps
return thepacbps
def hmmresults2splittedpacbps(results,
hmmcoords,
target,
informant,
inwpCBG,
input,
gapsize=2,
min_bitscore=0):
""" """
hmm_pacbporf_list = []
for hmmhit in results:
(sbjct_header, sbjct_start, sbjct_end, query_start, query_end, query,
match, sbjct, score, expect) = hmmhit
if score < min_bitscore: continue
_org, orfid = hmmhit[0].split('_orf_')
orfSbjct = input[informant]['orfs'].get_orf_by_id(int(orfid))
orfQuery = inwpCBG.get_orfs_of_graph(target)[0]
querycoords = (min(hmmcoords[target]), max(hmmcoords[target]))
key_data, hmmpacbporf = hmmhit2pacbp(orfQuery, target, querycoords,
orfSbjct, informant, hmmhit)
# check if hmmpacbporf creation was succesfull
if not hmmpacbporf: continue
# if here, unextend and split on gapsize
(pacbpkey, qNode, sNode) = key_data
hmmpacbporf.unextend_pacbporf()
splittedhmmpacbporfs, splittedstatus =\
split_pacb_on_gaps(hmmpacbporf,gapsize=gapsize)
# loop over the splitted ones and store high(er) scoring fractions
for splittedhmmpf in splittedhmmpacbporfs:
# added code to strip unmatched ends. Should not
# be neccesarily anymore, but just to be certain
# no leading/trailing gaps are there
# if '-' in [ splittedhmmpf.query[0], splittedhmmpf.sbjct[0],
# splittedhmmpf.query[-1], splittedhmmpf.sbjct[-1] ]:
# hmmpacbp = pacbporf2pacbp(splittedhmmpf)
# hmmpacbp.strip_unmatched_ends()
# if not hmmpacbp: continue
# if len(hmmpacbp) <= 1: continue
# # if here, make again a pacbporf of the pacbp
# splittedhmmpf = pacbp2pacbporf(hmmpacbp,splittedhmmpf.orfQ,splittedhmmpf.orfS)
if splittedhmmpf.bitscore < min_bitscore: continue
# check if query/sbjct must be swapped
queryNode = (target, orfQuery.id)
sbjctNode = (informant, orfSbjct.id)
if qNode == queryNode:
pass
elif qNode == sbjctNode:
# swap query and sbjct!
splittedhmmpf = swap_query_and_sbjct(splittedhmmpf)
else:
# whaaaat else !?
raise "UNEXPECTED EVENT"
# append to hmm_pacbporf_list
hmm_pacbporf_list.append(splittedhmmpf)
# return bitscore ordered list of hmmpacbporfs
return _order_list_by_attribute(hmm_pacbporf_list,
order_by='bitscore',
reversed=True)