def WORKING_sprdif2clustalw2cbg(cbg,sprdif,SCAFFOLD_GAP_OMSR_OFFSET=0,verbose=False):
""" """
# gather sequence concerning the scaffold gap of the mutual nodes
seqs, orfs, coords = {}, {}, {}
for node in sprdif.keys():
org = cbg.organism_by_node(node)
sta = min( sprdif[node] ) - SCAFFOLD_GAP_OMSR_OFFSET
end = max( sprdif[node] ) + SCAFFOLD_GAP_OMSR_OFFSET
orf = cbg.get_orfs_of_graph(organism=org)[0]
seq = orf.getaas(abs_pos_start=sta,abs_pos_end=end)
seqs[org] = seq
orfs[org] = orf
coords[org] = [sta,end]
# do clustalw and strip_alignment_for_exterior_gaps
(_algseqs,_algm) = clustalw(seqs=seqs)
####################################################################
if verbose: print seqs, "\n", _algseqs, "\n", _algm
####################################################################
_algseqs,_algm,coords = strip_alignment_for_exterior_gaps(_algseqs,_algm,coords)
if not _algm:
####################################################################
if verbose: print "NO ALGM.??\n", seqs, "\n", _algseqs, "\n", _algm
####################################################################
# alignment completely vanished by `strip_alignment_for_exterior_gaps`
return None
# do required import here (prevent circular imports)
from graphAbgp.graph_codingblock import CodingBlockGraph
from graphAbgp.exceptions import NoOverallMinimalSpanningRange
from pacb import conversion as pacbconversion
from lib_cexpander import cexpander_checkCBG4omsrbordergaps, ZeroUniformlyAlignedPositions
# translate the clustalw alignment into an artificial CBG
newcbg = CodingBlockGraph()
newcbg.add_nodes(sprdif.keys())
pacbp_is_none = False
for nodeA,nodeB in newcbg.pairwisecrosscombinations_node():
orgA = cbg.organism_by_node(nodeA)
orgB = cbg.organism_by_node(nodeB)
# _algseqs keys are organisms, not nodes!
alignment = ( _algseqs[orgA], _algm, _algseqs[orgB] )
paircoords = ( coords[orgA][0], coords[org][1], coords[orgB][0], coords[orgB][1] )
pacbp = pacbconversion.pacbp_from_clustalw(alignment=alignment,coords=paircoords)
if pacbp == None:
# pacbp is not creatable -> break i.o.t. return None
pacbp_is_none = True
break
pacbporf = pacbconversion.pacbp2pacbporf(pacbp,orfs[orgA],orfs[orgB])
wt = pacbporf.bitscore
pacbpkey = pacbporf.construct_unique_key(nodeA,nodeB)
newcbg.add_edge(nodeA,nodeB,wt=wt)
newcbg.pacbps[(pacbpkey,nodeA,nodeB)] = pacbporf
# check if all pacbporfs are created succesfully
if pacbp_is_none: return None
# update edge weight by OMSR and return
newcbg.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = 3
if newcbg.has_overall_minimal_spanning_range():
newcbg.update_edge_weights_by_minimal_spanning_range()
try:
newcbg.correct_pacbpgaps_nearby_omsr()
return newcbg
except NoOverallMinimalSpanningRange:
return None
#try:
# status = cexpander_checkCBG4omsrbordergaps(newcbg)
# return newcbg
#except NoOverallMinimalSpanningRange:
# return None
#except ZeroUniformlyAlignedPositions:
# return None
#except:
# return None
else:
return None
def clustalwinput2cbg(seqs,orfs,coords,nodes,
matrix = None,
minimal_overall_spanning_range_size = 3,
verbose=False):
"""
@type seqs: dict
@param seqs: dict with ORGANISM IDENTIFIER as keys, sequences as values
@type orfs: dict
@param orfs: dict with ORGANISM IDENTIFIER as keys, Orf objects as values
@type coords: dict
@param coords: dict with ORGANISM IDENTIFIER as keys, [ sta, end ] as values
@type nodes: list
@param nodes: list with nodes corresponding to the ORGANISM IDENTIFIER in the dictionaries
@attention: coordinates in coords should correspond to the sequneces in seqs!
"""
# do clustalw and strip_alignment_for_exterior_gaps
(algseqs,algm) = clustalw(seqs=seqs)
####################################################################
if verbose: print seqs, "\n", algseqs, "\n", algm, "\n", coords
####################################################################
_testalgseqs,_testalgm,_testcoords = strip_alignment_for_exterior_gaps(
deepcopy(algseqs),deepcopy(algm),deepcopy(coords))
if not _testalgm:
####################################################################
if verbose: print "NO ALGM\n", seqs, "\n", _testalgseqs, "\n", _testalgm
####################################################################
# alignment completely vanished by `strip_alignment_for_exterior_gaps`
return None
# do required import here (prevent circular imports)
from graphAbgp.graph_codingblock import CodingBlockGraph
from graphAbgp.exceptions import NoOverallMinimalSpanningRange
from pacb import conversion as pacbconversion
if not matrix:
raise "No ProteinSimilarityMatrix applied!"
# translate the clustalw alignment into an artificial CBG
newcbg = CodingBlockGraph()
newcbg.add_nodes(nodes)
pacbp_is_none = False
for nodeA,nodeB in newcbg.pairwisecrosscombinations_node():
orgA = newcbg.organism_by_node(nodeA)
orgB = newcbg.organism_by_node(nodeB)
# create stripped alignments for this pair of sequences
# do not forget to make deepcopies of the data structures!
subcoords = { orgA: coords[orgA], orgB: coords[orgB] }
subalgseqs = { orgA: algseqs[orgA], orgB: algseqs[orgB] }
_algseqs,_algm,_coords = strip_alignment_for_exterior_gaps(
deepcopy(subalgseqs),deepcopy(algm),deepcopy(subcoords) )
# recreate a pairwise ClustalW alignment string
_algm = make_clustalw_alignment_match(
_algseqs[orgA],_algseqs[orgB],
matrix = matrix.matrix )
# _algseqs keys are organisms, not nodes!
alignment = ( _algseqs[orgA], _algm, _algseqs[orgB] )
paircoords = ( _coords[orgA][0], _coords[orgA][1],
_coords[orgB][0], _coords[orgB][1] )
pacbp = pacbconversion.pacbp_from_clustalw(
alignment=alignment,coords=paircoords)
if pacbp == None:
# pacbp is not creatable -> break i.o.t. return None
pacbp_is_none = True
break
pacbporf = pacbconversion.pacbp2pacbporf(pacbp,orfs[orgA],orfs[orgB])
####################################################################
if verbose:
print orgA, orgB, pacbporf
for item in alignment: print item
print paircoords
####################################################################
wt = pacbporf.bitscore
pacbpkey = pacbporf.construct_unique_key(nodeA,nodeB)
newcbg.add_edge(nodeA,nodeB,wt=wt)
newcbg.pacbps[(pacbpkey,nodeA,nodeB)] = pacbporf
# check if all pacbporfs are created succesfully
if pacbp_is_none: return None
# update edge weight by OMSR and return
newcbg.MINIMAL_OVERAL_SPANNING_RANGE_SIZE =\
minimal_overall_spanning_range_size
if newcbg.has_overall_minimal_spanning_range():
newcbg.update_edge_weights_by_minimal_spanning_range()
try:
newcbg.correct_pacbpgaps_nearby_omsr()
return newcbg
except NoOverallMinimalSpanningRange:
return None
else:
return None
def WORKING_sprdif2clustalw2cbg(cbg,sprdif,SCAFFOLD_GAP_OMSR_OFFSET=1,verbose=False):
""" """
# gather sequence concerning the scaffold gap of the mutual nodes
seqs, orfs, coords = {}, {}, {}
for node in sprdif.keys():
org = cbg.organism_by_node(node)
sta = min( sprdif[node] ) - SCAFFOLD_GAP_OMSR_OFFSET
end = max( sprdif[node] ) + SCAFFOLD_GAP_OMSR_OFFSET
orf = cbg.get_orfs_of_graph(organism=org)[0]
# correct a priori for out-of-range exceptions
# due to SCAFFOLD_GAP_OMSR_OFFSET
sta = max([ sta, orf.protein_startPY ])
end = min([ end, orf.protein_endPY ])
seq = orf.getaas(abs_pos_start=sta,abs_pos_end=end)
seqs[org] = seq
orfs[org] = orf
coords[org] = [sta,end]
# do clustalw and strip_alignment_for_exterior_gaps
(algseqs,algm) = clustalw(seqs=seqs)
####################################################################
if verbose: print seqs, "\n", algseqs, "\n", algm, "\n", coords
####################################################################
_testalgseqs,_testalgm,_testcoords = strip_alignment_for_exterior_gaps(
deepcopy(algseqs),deepcopy(algm),deepcopy(coords))
if not _testalgm:
####################################################################
if verbose: print "NO ALGM\n", seqs, "\n", _testalgseqs, "\n", _testalgm
####################################################################
# alignment completely vanished by `strip_alignment_for_exterior_gaps`
return None
# do required import here (prevent circular imports)
from graphAbgp.graph_codingblock import CodingBlockGraph
from graphAbgp.exceptions import NoOverallMinimalSpanningRange
from pacb import conversion as pacbconversion
from lib_cexpander import cexpander_checkCBG4omsrbordergaps, ZeroUniformlyAlignedPositions
# translate the clustalw alignment into an artificial CBG
newcbg = CodingBlockGraph()
newcbg.add_nodes(sprdif.keys())
pacbp_is_none = False
for nodeA,nodeB in newcbg.pairwisecrosscombinations_node():
orgA = cbg.organism_by_node(nodeA)
orgB = cbg.organism_by_node(nodeB)
# create stripped alignments for this pair of sequences
# do not forget to make deepcopies of the data structures!
subcoords = { orgA: coords[orgA], orgB: coords[orgB] }
subalgseqs = { orgA: algseqs[orgA], orgB: algseqs[orgB] }
_algseqs,_algm,_coords = strip_alignment_for_exterior_gaps(
deepcopy(subalgseqs),deepcopy(algm),deepcopy(subcoords) )
# get a/the ProteinSimilarityMatrix from the original PacbP(ORF)
# and then recreate a pairwise ClustalW alignment string
protsimmtrx = cbg.get_pacbps_by_nodes(node1=nodeA,node2=nodeB)[0].MATRIX
_algm = make_clustalw_alignment_match(
_algseqs[orgA],_algseqs[orgB],
matrix = protsimmtrx.matrix )
# _algseqs keys are organisms, not nodes!
alignment = ( _algseqs[orgA], _algm, _algseqs[orgB] )
paircoords = ( _coords[orgA][0], _coords[orgA][1],
_coords[orgB][0], _coords[orgB][1] )
pacbp = pacbconversion.pacbp_from_clustalw(
alignment=alignment,coords=paircoords)
if pacbp == None:
# pacbp is not creatable -> break i.o.t. return None
pacbp_is_none = True
break
pacbporf = pacbconversion.pacbp2pacbporf(pacbp,orfs[orgA],orfs[orgB])
####################################################################
if verbose:
print orgA, orgB, pacbporf
for item in alignment: print item
print paircoords
####################################################################
wt = pacbporf.bitscore
pacbpkey = pacbporf.construct_unique_key(nodeA,nodeB)
newcbg.add_edge(nodeA,nodeB,wt=wt)
newcbg.pacbps[(pacbpkey,nodeA,nodeB)] = pacbporf
# check if all pacbporfs are created succesfully
if pacbp_is_none: return None
# update edge weight by OMSR and return
newcbg.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = 3
if newcbg.has_overall_minimal_spanning_range():
newcbg.update_edge_weights_by_minimal_spanning_range()
try:
newcbg.correct_pacbpgaps_nearby_omsr()
return newcbg
except NoOverallMinimalSpanningRange:
return None
else:
return None