def get_reverse_cbg(cbg,frame,verbose=False):
"""
Get the ReversecomplementCodingBlockGraph in requested frame of this CBG
@type cbg: CodingBlockGraph
@param cbg: CodingBlockGraph to reversecomplement
@type frame: integer
@param frame: 0,1 or 2
@type verbose: Boolean
@param verbose: print intermediate info to STDOUT for debugging purposes
@rtype: ReversecomplementCodingBlockGraph or None
@return: ReversecomplementCodingBlockGraph (when existing) or None
"""
min_orf_length = (cbg.omsrlength()/2)*3
orfs = get_reverse_strand_orfsets(cbg,frame,min_orf_length=min_orf_length)
# remap the identifiers of the orf objects i.o.t....
multifastas = {}
blastdbs = {}
pacbpcol = PacbpCollectionGraph()
dpcpacbpcol = PacbpCollectionGraph() # ``deepcopied`` variant for pacbps
for org in orfs.keys():
fname = "%s_reversecbg_%s.mfa" % (org,cbg.barcode())
writeMultiFasta(orfs[org].tofastadict(),fname)
multifastas[org] = fname
########################################################################
if verbose:
print "ORFS:", org, len(orfs[org].orfs),
print [len(o.protein_sequence) for o in orfs[org].orfs ]
########################################################################
revpacbps = {}
for orgQ,orgS in cbg.pairwisecrosscombinations_organism():
# create blastdb if it does not exist yet
if not blastdbs.has_key(orgS):
formatdb(fname=multifastas[orgS])
blastdbs[orgS] = multifastas[orgS]
revpacbporfs = {}
for orfQ in orfs[orgQ].orfs:
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,orfQ.protein_sequence,
dbname="./"+blastdbs[orgS])
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# obtain coordinates from sbjct orf identifier
orfS = orfs[orgS].get_orf_by_id(alignment.title.replace(">",""))
# take only the *best* HSP (highest scoring first one)
hsp = alignment.hsps[0]
# skip if hsp is very short
if len(hsp.query) < cbg.omsrlength()/2: continue
# correct to absolute positions
hsp.query_start = hsp.query_start + orfQ.protein_startPY
hsp.sbjct_start = hsp.sbjct_start + orfS.protein_startPY
# initialize the PacbP
pacbporf = pacb.conversion.pacbp2pacbporf(
pacb.PacbP(blastp_hsp=hsp),orfQ,orfS)
################################################################
if verbose:
print pacbporf, orgQ,orgS, orfQ
print pacbporf.query
print pacbporf.match
print pacbporf.sbjct
###pacbporf.print_protein_and_dna()
################################################################
nodeQ = ( orgQ, orfQ.protein_startPY )
nodeS = ( orgS, orfS.protein_startPY )
uqkey = pacbporf.construct_unique_key(nodeQ,nodeS)
if not nodeQ in pacbpcol.get_nodes(): pacbpcol.add_node(nodeQ)
if not nodeS in pacbpcol.get_nodes(): pacbpcol.add_node(nodeS)
pacbpcol.add_edge(nodeQ,nodeS,wt=pacbporf.bitscore)
# store to dpcpacbpcol -> pacbpcol is broken in pieces lateron!
dpcpacbpcol.pacbps[(uqkey,nodeQ,nodeS)] = pacbporf
# file cleanup
_file_cleanup(multifastas.values())
_file_cleanup(["formatdb.log"])
_file_cleanup([ fname+".*" for fname in blastdbs.values()])
if not pacbpcol.organism_set_size() == cbg.organism_set_size():
# no CBG on the reverse strand
return None
# ``deepcopy`` PacbPcollection
dpcpacbpcol.add_nodes( pacbpcol.get_nodes() )
for (uqkey,nodeQ,nodeS) in dpcpacbpcol.pacbps.keys():
(bitscore,length,orfQid,orfSid) = uqkey
dpcpacbpcol.add_edge(nodeQ,nodeS,wt=bitscore)
############################################################################
if verbose:
print pacbpcol, "bitscores:",
print [ pacbporf.bitscore for pacbporf in dpcpacbpcol.pacbps.values() ]
############################################################################
# do some transformations on the pacbpcol
pacbpcol.remove_low_connectivity_nodes(min_connectivity=cbg.node_count()-1)
splittedCBGs = pacbpcol.find_fully_connected_subgraphs(
edges=cbg.node_count()-1 , max_missing_edges=0 )
# convert to list of CBGs and do some transformations
cbgList = ListOfCodingBlockGraphs(splittedCBGs,input={},crossdata={})
cbgList.remove_all_but_complete_cbgs()
cbgList.harvest_pacbps_from_pacbpcollection(dpcpacbpcol)
cbgList.remove_cbgs_without_omsr()
cbgList.update_edge_weights_by_minimal_spanning_range()
cbgList.order_list_by_attribute(order_by='total_weight',reversed=True)
############################################################################
if verbose:
for revcbg in cbgList:
print "revCBG:", revcbg
############################################################################
if not cbgList:
# no CBG on the reverse strand
return None
else:
# return the highest scoring CBG as a ReversecomlementCodingBlockGraph
return CodingBlockGraph2ReversecomlementCodingBlockGraph(
cbgList.codingblockgraphs[0])
def createblastdbs(input,
GSG,
OPTIONS,
dbfraction=None,
organism=None,
acceptorfids=[],
rejectorfids=[]):
"""
(Re)create blast-db's by masking the areas thar are incorporated in the GSG
@type input: dict
@param input: `input` data structure dictionary
@type GSG: GenestructureOfCodingBlockGraphs
@param GSG: GenestructureOfCodingBlockGraphs instance
@type OPTIONS: optparse options instance
@param OPTIONS: optparse options instance (with attribute 'abinitio')
@type dbfraction: string
@param dbfraction: None, 'all', 'GSGupstream', 'GSGcentral', 'GSGdownstream', 'annotation'
@type organism: organism identifier
@param organism: only recreate blastdb for this organism/gene identifier
@type acceptorfids: list with integers
@param acceptorfids: list of orf ids to accept
@type rejectorfids: list with integers
@param rejectorfids: list of orf ids to reject
@attention: acceptorfids and rejectorfids are only used when organism is specified!
"""
seqsindb = {}
for org in input.keys():
# if organism is given, do only this one
if organism and org != organism: continue
# acceptorfids anc rejectorfids only valid in combi with `organism`
if not organism: acceptorfids, rejectorfids = [], []
# assign blast database name / multi fasta file and open filehandle
uniquetag = get_random_string_tag()
fname = '%s-blastdb-%s.fa' % (uniquetag, org)
fullpath = osPathJoin(OPTIONS.outdir, fname)
fh = open(fullpath, 'w')
seqsindb[org] = 0
# distinct cases possible:
if len(GSG):
# there is already a GSG, so this is not the first blast iteration
# do not apply a shortcut when OPTIONS.abinitio == False
coords = GSG.omsr2mask(org)
if dbfraction == 'GSGupstream':
# take only orfs LEFT of the first CBG in GSG
max_orf_nt_start = max(
GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
elif dbfraction == 'GSGdownstream':
# take only orfs RIGTH of the last CBG in GSG
min_orf_nt_end = min(
GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
min_orf_end=min_orf_nt_end,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
elif dbfraction == 'GSGcentral':
# take only orfs in between FIRST and LAST CBG in GSG (can be only one CBG!)
max_orf_nt_start = max(
GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
min_orf_nt_end = min(
GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(
min_orf_end=min_orf_nt_end,
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,
rejectorfids=rejectorfids)
else:
# dbfraction equals 'all' or None -> no limitation, just take all orfs!
# do only the general limitation on sublists of orfids
orflist = input[org]['orfs'].get_elegiable_orfs(
acceptorfids=acceptorfids, rejectorfids=rejectorfids)
# create masked fasta of this sequence part only
newfasta = input[org]['orfs'].tomaskedfasta(coords=coords,
orflist=orflist,
header_prefix=org)
# write to file and count accessions in this file -> seqsindb[org]
fh.write(newfasta)
seqsindb[org] = newfasta.count(">")
else:
# No filled GSG objects -> no a priori knowledge yet
# When dbfraction=='annotated' and !OPTIONS.abinitio -> take annotated orfs only
# TODO: dbfraction is not checked/used here -> just OPTIONS.abinitio
for orf in input[org]['orfs'].orfs:
# in case not abinitio, make only a db of orfs in teh current annotation!
if OPTIONS.abinitio == False and orf.id not in input[org][
'orfid-genestructure']:
continue
if orf.id in rejectorfids:
# ignore Orfs that are listed as to-be-ignored
continue
if acceptorfids and orf.id not in acceptorfids:
# ignore Orfs that are not listed as to-be-accepted
continue
# write fasta of orf to file
fh.write(
orf.tofasta(header="%s_orf_%s" % (org, orf.id)) + "\n")
# increase seqsindb[org] counter
seqsindb[org] += 1
# close the filehandle
fh.close()
# run formatdb
formatdb(fname=fullpath)
# set name of blastdb in infodict
input[org]['blastdb'] = fullpath
# return the counter of how much orf sequences are stored in the blast database
return seqsindb
def get_frameshifted_cbg(cbg, input, verbose=True):
"""
Get a CBG with frameshifts (in some of if Orfs) compared to this CBG
@type cbg: CodingBlockGraph
@param cbg: CodingBlockGraph to check for frameshifts
@type input: dict
@param input: input <dict data structure> with lists of Orfs
@type verbose: Boolean
@param verbose: print intermediate info to STDOUT for debugging purposes
@rtype: CodingBlockGraph or None
@return: CodingBlockGraph (when existing) or None
"""
# get elegiable lists of Orfs
orfs = _get_elegiable_frameshift_orfsets(cbg, input)
# check how many Orfs are elgiable...
if sum([len(l.orfs) for l in orfs.values()]) == cbg.node_count():
# no frameshift possible here...
return None
# remap the identifiers of the orf objects i.o.t....
multifastas = {}
blastdbs = {}
pacbpcol = PacbpCollectionGraph()
dpcpacbpcol = PacbpCollectionGraph() # ``deepcopied`` variant for pacbps
for org in orfs.keys():
# REMAP fastaheaders as ids to retrieve the Orfs after blast..
for orf in orfs[org].orfs:
orf.fastaheader = str(orf.id)
fname = "%s_frameshiftcbg_%s.mfa" % (org, cbg.barcode())
writeMultiFasta(orfs[org].tofastadict(), fname)
multifastas[org] = fname
########################################################################
if verbose:
print "ORFS:", org, len(orfs[org].orfs),
print[orf.id for orf in orfs[org].orfs],
print[str(orf) for orf in orfs[org].orfs]
########################################################################
for orgQ, orgS in cbg.pairwisecrosscombinations_organism():
# create blastdb if it does not exist yet
if not blastdbs.has_key(orgS):
formatdb(fname=multifastas[orgS])
blastdbs[orgS] = multifastas[orgS]
for orfQ in orfs[orgQ].orfs:
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,
orfQ.protein_sequence,
dbname="./" + blastdbs[orgS])
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# obtain coordinates from sbjct orf identifier
orfid = alignment.title.replace(">", "").split(" ")[0].replace(
"_", "")
orfS = orfs[orgS].get_orf_by_id(int(orfid))
nodeQ = (orgQ, orfQ.id)
nodeS = (orgS, orfS.id)
if nodeQ in cbg.get_nodes() and nodeS in cbg.get_nodes():
pacbporf = cbg.get_pacbps_by_nodes(node1=nodeQ,
node2=nodeS)[0]
else:
# take only the *best* HSP (highest scoring first one)
hsp = alignment.hsps[0]
# correct to absolute positions
hsp.query_start = hsp.query_start + orfQ.protein_startPY
hsp.sbjct_start = hsp.sbjct_start + orfS.protein_startPY
# initialize the PacbP
pacbporf = pacb.conversion.pacbp2pacbporf(
pacb.PacbP(blastp_hsp=hsp), orfQ, orfS)
############################################################
if verbose: print "NEW:", pacbporf
############################################################
uqkey = pacbporf.construct_unique_key(nodeQ, nodeS)
if not nodeQ in pacbpcol.get_nodes(): pacbpcol.add_node(nodeQ)
if not nodeS in pacbpcol.get_nodes(): pacbpcol.add_node(nodeS)
pacbpcol.add_edge(nodeQ, nodeS, wt=pacbporf.bitscore)
# store to dpcpacbpcol -> pacbpcol is broken in pieces lateron!
dpcpacbpcol.pacbps[(uqkey, nodeQ, nodeS)] = pacbporf
# file cleanup
_file_cleanup(multifastas.values())
_file_cleanup(["formatdb.log"])
_file_cleanup([fname + ".*" for fname in blastdbs.values()])
if not pacbpcol.organism_set_size() == cbg.organism_set_size():
############################################################
if verbose: print "org_set_size() PCG < CBG"
############################################################
# no CBG on the reverse strand
return None
# ``deepcopy`` PacbPcollection
dpcpacbpcol.add_nodes(pacbpcol.get_nodes())
for (uqkey, nodeQ, nodeS) in dpcpacbpcol.pacbps.keys():
(bitscore, length, orfQid, orfSid) = uqkey
dpcpacbpcol.add_edge(nodeQ, nodeS, wt=bitscore)
############################################################################
if verbose:
print pacbpcol, "bitscores:",
print[pacbporf.bitscore for pacbporf in dpcpacbpcol.pacbps.values()]
############################################################################
# do some transformations on the pacbpcol
pacbpcol.remove_low_connectivity_nodes(min_connectivity=cbg.node_count() -
1)
splittedCBGs = pacbpcol.find_fully_connected_subgraphs(
edges=cbg.node_count() - 1, max_missing_edges=0)
# convert to list of CBGs and do some transformations
cbgList = ListOfCodingBlockGraphs(splittedCBGs, input={}, crossdata={})
cbgList.remove_all_but_cbgs()
cbgList.remove_cbgs_with_lt_nodes(cbg.node_count())
cbgList.harvest_pacbps_from_pacbpcollection(dpcpacbpcol)
cbgList.remove_cbgs_without_omsr()
cbgList.update_edge_weights_by_minimal_spanning_range()
cbgList.order_graphlist_by_total_weight_and_identity()
############################################################################
if verbose:
print "FScbgs (%s)" % len(cbgList)
for fscbg in cbgList:
print fscbg
############################################################################
if not cbgList:
# no (better) frameshifted CBG
return None
elif cbgList and not cbgList[0].node_set().symmetric_difference(
cbg.node_set()):
# best CBG is not frameshifted, but CBG itself
return None
else:
# score the difference between the frameshifted and current CBG
score_cbg = cbg.total_weight() * cbg.omsr_identityscore()
score_fscbg = cbgList[0].total_weight(
) * cbgList[0].omsr_identityscore()
# check overlap between the frameshifted and current CBG
a, b, c, d, e, f, g = relatively_positioned_towards(cbgList[0], cbg)
########################################################################
if verbose:
print "CBG", cbg
cbg.printmultiplealignment()
for fscbg in cbgList:
print "fsCBG:", fscbg
fscbg.printmultiplealignment()
########################################################################
if (c, d) == ((0, 0, 1), (1, 0, 0)) or (c, d) == ((0, 0, 1),
(1, 0, 0)):
# CBG and frameshifted CBG do not share a single AA overlap...
# This does not represent a frameshifted CBG as we searched for
return False
elif score_fscbg > score_cbg:
# return the highest scoring, frameshifted CBG
return cbgList[0]
else:
# no, still not convinced that this is a frameshifted CBG
return False
def createblastdbs(input,GSG,OPTIONS,dbfraction=None,organism=None,acceptorfids=[],rejectorfids=[]):
"""
(Re)create blast-db's by masking the areas thar are incorporated in the GSG
@type input: dict
@param input: `input` data structure dictionary
@type GSG: GenestructureOfCodingBlockGraphs
@param GSG: GenestructureOfCodingBlockGraphs instance
@type OPTIONS: optparse options instance
@param OPTIONS: optparse options instance (with attribute 'abinitio')
@type dbfraction: string
@param dbfraction: None, 'all', 'GSGupstream', 'GSGcentral', 'GSGdownstream', 'annotation'
@type organism: organism identifier
@param organism: only recreate blastdb for this organism/gene identifier
@type acceptorfids: list with integers
@param acceptorfids: list of orf ids to accept
@type rejectorfids: list with integers
@param rejectorfids: list of orf ids to reject
@attention: acceptorfids and rejectorfids are only used when organism is specified!
"""
seqsindb = {}
for org in input.keys():
# if organism is given, do only this one
if organism and org!=organism: continue
# acceptorfids anc rejectorfids only valid in combi with `organism`
if not organism: acceptorfids, rejectorfids = [], []
# assign blast database name / multi fasta file and open filehandle
uniquetag = get_random_string_tag()
fname = '%s-blastdb-%s.fa' % (uniquetag,org)
fullpath = osPathJoin(OPTIONS.outdir,fname)
fh = open(fullpath,'w')
seqsindb[org] = 0
# distinct cases possible:
if len(GSG):
# there is already a GSG, so this is not the first blast iteration
# do not apply a shortcut when OPTIONS.abinitio == False
coords = GSG.omsr2mask(org)
if dbfraction == 'GSGupstream':
# take only orfs LEFT of the first CBG in GSG
max_orf_nt_start = max(GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
elif dbfraction == 'GSGdownstream':
# take only orfs RIGTH of the last CBG in GSG
min_orf_nt_end = min(GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(min_orf_end=min_orf_nt_end,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
elif dbfraction == 'GSGcentral':
# take only orfs in between FIRST and LAST CBG in GSG (can be only one CBG!)
max_orf_nt_start = max(GSG[-1].overall_minimal_spanning_range(organism=org)) * 3
min_orf_nt_end = min(GSG[0].overall_minimal_spanning_range(organism=org)) * 3
orflist = input[org]['orfs'].get_elegiable_orfs(min_orf_end=min_orf_nt_end,
max_orf_start=max_orf_nt_start,
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
else:
# dbfraction equals 'all' or None -> no limitation, just take all orfs!
# do only the general limitation on sublists of orfids
orflist = input[org]['orfs'].get_elegiable_orfs(
acceptorfids=acceptorfids,rejectorfids=rejectorfids)
# create masked fasta of this sequence part only
newfasta = input[org]['orfs'].tomaskedfasta(coords=coords,orflist=orflist,header_prefix=org)
# write to file and count accessions in this file -> seqsindb[org]
fh.write(newfasta)
seqsindb[org] = newfasta.count(">")
else:
# No filled GSG objects -> no a priori knowledge yet
# When dbfraction=='annotated' and !OPTIONS.abinitio -> take annotated orfs only
# TODO: dbfraction is not checked/used here -> just OPTIONS.abinitio
for orf in input[org]['orfs'].orfs:
# in case not abinitio, make only a db of orfs in teh current annotation!
if OPTIONS.abinitio == False and orf.id not in input[org]['orfid-genestructure']:
continue
if orf.id in rejectorfids:
# ignore Orfs that are listed as to-be-ignored
continue
if acceptorfids and orf.id not in acceptorfids:
# ignore Orfs that are not listed as to-be-accepted
continue
# write fasta of orf to file
fh.write(orf.tofasta(header="%s_orf_%s" % (org,orf.id))+"\n")
# increase seqsindb[org] counter
seqsindb[org]+=1
# close the filehandle
fh.close()
# run formatdb
formatdb(fname=fullpath)
# set name of blastdb in infodict
input[org]['blastdb'] = fullpath
# return the counter of how much orf sequences are stored in the blast database
return seqsindb
def blastanalysescbgjunction(
gsg,
prevCBG,
nextCBG,
omit_cbg_orfs=False,
omit_non_cbg_orfs=False,
extra_blastp_params=CBG_JUNCTION_BLAST2PACBPCOL_EXTRA_BLASTP_PARAMS,
omsr_2_mask_aa_length_correction=CBG_JUNCTION_BLAST2PACBPCOL_OMSR_2_AA_MASK,
verbose=False):
"""
"""
############################################################
if verbose:
stw = StopWatch('blastanalysescbgjunction')
stw.start()
############################################################
orfs = {}
if not omit_cbg_orfs:
# gather Orfs from prevCBG and nextCBG
for org, orflist, in prevCBG.get_orfs_of_graph().iteritems():
orf = orflist[0]
orfs[(org, orf.id)] = orf
for org, orflist, in nextCBG.get_orfs_of_graph().iteritems():
orf = orflist[0]
orfs[(org, orf.id)] = orf
############################################################
if verbose:
print stw.lap(), "orfs (1):", len(orfs)
print _format_orf_nodes_to_string(orfs.keys())
############################################################
# create masked fasta database in a dict
fastadbmfa = parseFasta(
create_hmmdb_for_neighbouring_cbgs(
gsg.input,
prevCBG,
nextCBG,
omsr_2_mask_aa_length_correction=omsr_2_mask_aa_length_correction,
).split("\n"))
############################################################
if verbose: print stw.lap(), "fasta db (1):", len(fastadbmfa)
############################################################
# remove ORFs that do not belong to prevCBG and nextCBG,
# or that DO belong to prevCBG and nextCBG, or neither
fastaheaders = fastadbmfa.keys()
for header in fastaheaders:
org, orfid = header.split("_orf_")
orfid = int(orfid)
node = (org, orfid)
# check for the omit_non_cbg_orfs criterion
add_orf = False
if omit_non_cbg_orfs:
if node not in orfs:
del (fastadbmfa[header])
else:
add_orf = True
# check for the omit_cbg_orfs criterion
if omit_cbg_orfs and node in orfs:
del (fastadbmfa[header])
if add_orf:
# get this Orf and add to orfs
orfs[node] = gsg.input[org]['orfs'].get_orf_by_id(orfid)
############################################################
if verbose:
print stw.lap(), "fasta db (2):", len(fastadbmfa)
print _format_fastadbmfa_nodes_to_string(fastadbmfa.keys())
############################################################
############################################################
if verbose:
print stw.lap(), "orfs (2):", len(orfs)
print _format_orf_nodes_to_string(orfs.keys())
############################################################
# no query/sbjct range left at all
if not fastadbmfa: return []
# check if all organisms are still covered
orgSet = Set([k.split("_orf_")[0] for k in fastadbmfa.keys()])
if orgSet.symmetric_difference(gsg.organism_set()):
return []
# create !single! fasta database
fastadbname = prevCBG.barcode() + "_" + nextCBG.barcode() + ".mfa"
writeMultiFasta(fastadbmfa, fastadbname)
formatdb(fname=fastadbname)
# remap the identifiers of the orf objects i.o.t....
multifastas = {}
blastdbs = {}
pacbpcol = PacbpCollectionGraph()
dpcpacbpcol = PacbpCollectionGraph() # ``deepcopied`` variant for pacbps
############################################################
if verbose: print stw.lap(), "blastp starting"
############################################################
for orgQ, orgS in prevCBG.pairwisecrosscombinations_organism():
for nodeQ, orfQ in orfs.iteritems():
# only blast the (masked) Orfs of orgQ
if prevCBG.organism_by_node(nodeQ) != orgQ: continue
# get the masked protein sequence of this orfObj
header = orgQ + "_orf_" + str(orfQ.id)
# check if key exists in fastadbmfa. In a case where
# an Orf is masked out completely, it is absent here!
if not fastadbmfa.has_key(header): continue
protseq = fastadbmfa[orgQ + "_orf_" + str(orfQ.id)]
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,
protseq,
fastadbname,
extra_blastp_params=extra_blastp_params)
# omit empty blast records
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# get sbjct Org and Orf identifiers
_orgS, _orfSid = alignment.title.replace(">",
"").split("_orf_")
if _orgS != orgS: continue
nodeS = (_orgS, int(_orfSid))
orfS = orfs[nodeS]
# take only the *best* HSP (highest scoring first one)
hsp = alignment.hsps[0]
# correct to absolute positions
hsp.query_start = hsp.query_start + orfQ.protein_startPY
hsp.sbjct_start = hsp.sbjct_start + orfS.protein_startPY
# initialize the PacbP
pacbporf = pacb.conversion.pacbp2pacbporf(
pacb.PacbP(blastp_hsp=hsp), orfQ, orfS)
################################################################
if verbose:
print pacbporf, orgQ, orgS, orfQ
print pacbporf.query
print pacbporf.match
print pacbporf.sbjct
################################################################
# create nodes; ( Organism Identifier, Orf Identifier )
nodeQ = (orgQ, orfQ.id)
nodeS = (orgS, orfS.id)
uqkey = pacbporf.construct_unique_key(nodeQ, nodeS)
if not nodeQ in pacbpcol.get_nodes(): pacbpcol.add_node(nodeQ)
if not nodeS in pacbpcol.get_nodes(): pacbpcol.add_node(nodeS)
pacbpcol.add_edge(nodeQ, nodeS, wt=pacbporf.bitscore)
# store to dpcpacbpcol -> pacbpcol is broken in pieces lateron!
dpcpacbpcol.pacbps[(uqkey, nodeQ, nodeS)] = pacbporf
############################################################
if verbose: print stw.lap(), "blastp done"
############################################################
# file cleanup
_file_cleanup(multifastas.values())
_file_cleanup(["formatdb.log"])
_file_cleanup([fname + ".*" for fname in blastdbs.values()])
# check if all Organism/Gene identifiers are covered in PacbPs
if not pacbpcol.organism_set_size() == gsg.organism_set_size():
return []
# ``deepcopy`` PacbPcollection pacbpcol to dpcpacbpcol
# In dpcpacbpcol the actual PacbPORFs are stores & kept,
# whereas pacbpcol itself is splitted in CBGs (which
# function does not yet (!?) take the actual pacbps into account)
dpcpacbpcol.add_nodes(pacbpcol.get_nodes())
for (uqkey, nodeQ, nodeS) in dpcpacbpcol.pacbps.keys():
(bitscore, length, orfQid, orfSid) = uqkey
dpcpacbpcol.add_edge(nodeQ, nodeS, wt=bitscore)
################################################################
if verbose:
print pacbpcol
print "PCG bitscores:",
print[p.bitscore for p in dpcpacbpcol.pacbps.values()]
print "PCG nodes:", dpcpacbpcol.get_ordered_nodes()
################################################################
#### do some transformations on the pacbpcol
####pacbpcol.remove_low_connectivity_nodes(min_connectivity=gsg.EXACT_SG_NODE_COUNT-1)
####splittedCBGs = pacbpcol.find_fully_connected_subgraphs(
#### edges=gsg.node_count()-1 , max_missing_edges=0 )
##### convert to list of CBGs and do some transformations
####cbgList = ListOfCodingBlockGraphs(splittedCBGs,input={},crossdata={})
####cbgList.remove_all_but_complete_cbgs()
####cbgList.remove_cbgs_with_lt_nodes(gsg.EXACT_SG_NODE_COUNT)
####cbgList.harvest_pacbps_from_pacbpcollection(dpcpacbpcol)
####cbgList.remove_cbgs_without_omsr()
####cbgList.update_edge_weights_by_minimal_spanning_range()
####cbgList.order_list_by_attribute(order_by='total_weight',reversed=True)
min_connectivity = max([1, gsg.EXACT_SG_NODE_COUNT - 1 - 2])
pacbpcol.remove_low_connectivity_nodes(min_connectivity=min_connectivity)
max_missing_edges = gsg.EXACT_SG_NODE_COUNT - 3
splittedCBGs = pacbpcol.find_fully_connected_subgraphs(
edges=gsg.node_count() - 1, max_missing_edges=max_missing_edges)
# convert to list of CBGs and do some transformations
cbgList = ListOfCodingBlockGraphs(splittedCBGs, input={}, crossdata={})
cbgList.remove_all_but_cbgs()
cbgList.harvest_pacbps_from_pacbpcollection(dpcpacbpcol)
cbgList.make_pacbps_for_missing_edges()
cbgList.remove_all_but_complete_cbgs()
cbgList.remove_cbgs_with_lt_nodes(gsg.EXACT_SG_NODE_COUNT)
cbgList.remove_cbgs_without_omsr()
cbgList.update_edge_weights_by_minimal_spanning_range()
cbgList.order_list_by_attribute(order_by='total_weight', reversed=True)
# and create_cache() for these CBGs
for cbg in cbgList:
cbg.create_cache()
####################################################################
if verbose:
print stw.lap(), "CBGs created", len(cbgList)
for newcbg in cbgList:
print "new:", newcbg
####################################################################
# return list with CBGs
return cbgList.codingblockgraphs
def get_reverse_cbg(cbg, frame, verbose=False):
"""
Get the ReversecomplementCodingBlockGraph in requested frame of this CBG
@type cbg: CodingBlockGraph
@param cbg: CodingBlockGraph to reversecomplement
@type frame: integer
@param frame: 0,1 or 2
@type verbose: Boolean
@param verbose: print intermediate info to STDOUT for debugging purposes
@rtype: ReversecomplementCodingBlockGraph or None
@return: ReversecomplementCodingBlockGraph (when existing) or None
"""
min_orf_length = (cbg.omsrlength() / 2) * 3
orfs = get_reverse_strand_orfsets(cbg,
frame,
min_orf_length=min_orf_length)
# remap the identifiers of the orf objects i.o.t....
multifastas = {}
blastdbs = {}
pacbpcol = PacbpCollectionGraph()
dpcpacbpcol = PacbpCollectionGraph() # ``deepcopied`` variant for pacbps
for org in orfs.keys():
fname = "%s_reversecbg_%s.mfa" % (org, cbg.barcode())
writeMultiFasta(orfs[org].tofastadict(), fname)
multifastas[org] = fname
########################################################################
if verbose:
print "ORFS:", org, len(orfs[org].orfs),
print[len(o.protein_sequence) for o in orfs[org].orfs]
########################################################################
revpacbps = {}
for orgQ, orgS in cbg.pairwisecrosscombinations_organism():
# create blastdb if it does not exist yet
if not blastdbs.has_key(orgS):
formatdb(fname=multifastas[orgS])
blastdbs[orgS] = multifastas[orgS]
revpacbporfs = {}
for orfQ in orfs[orgQ].orfs:
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,
orfQ.protein_sequence,
dbname="./" + blastdbs[orgS])
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# obtain coordinates from sbjct orf identifier
orfS = orfs[orgS].get_orf_by_id(
alignment.title.replace(">", ""))
# take only the *best* HSP (highest scoring first one)
hsp = alignment.hsps[0]
# skip if hsp is very short
if len(hsp.query) < cbg.omsrlength() / 2: continue
# correct to absolute positions
hsp.query_start = hsp.query_start + orfQ.protein_startPY
hsp.sbjct_start = hsp.sbjct_start + orfS.protein_startPY
# initialize the PacbP
pacbporf = pacb.conversion.pacbp2pacbporf(
pacb.PacbP(blastp_hsp=hsp), orfQ, orfS)
################################################################
if verbose:
print pacbporf, orgQ, orgS, orfQ
print pacbporf.query
print pacbporf.match
print pacbporf.sbjct
###pacbporf.print_protein_and_dna()
################################################################
nodeQ = (orgQ, orfQ.protein_startPY)
nodeS = (orgS, orfS.protein_startPY)
uqkey = pacbporf.construct_unique_key(nodeQ, nodeS)
if not nodeQ in pacbpcol.get_nodes(): pacbpcol.add_node(nodeQ)
if not nodeS in pacbpcol.get_nodes(): pacbpcol.add_node(nodeS)
pacbpcol.add_edge(nodeQ, nodeS, wt=pacbporf.bitscore)
# store to dpcpacbpcol -> pacbpcol is broken in pieces lateron!
dpcpacbpcol.pacbps[(uqkey, nodeQ, nodeS)] = pacbporf
# file cleanup
_file_cleanup(multifastas.values())
_file_cleanup(["formatdb.log"])
_file_cleanup([fname + ".*" for fname in blastdbs.values()])
if not pacbpcol.organism_set_size() == cbg.organism_set_size():
# no CBG on the reverse strand
return None
# ``deepcopy`` PacbPcollection
dpcpacbpcol.add_nodes(pacbpcol.get_nodes())
for (uqkey, nodeQ, nodeS) in dpcpacbpcol.pacbps.keys():
(bitscore, length, orfQid, orfSid) = uqkey
dpcpacbpcol.add_edge(nodeQ, nodeS, wt=bitscore)
############################################################################
if verbose:
print pacbpcol, "bitscores:",
print[pacbporf.bitscore for pacbporf in dpcpacbpcol.pacbps.values()]
############################################################################
# do some transformations on the pacbpcol
pacbpcol.remove_low_connectivity_nodes(min_connectivity=cbg.node_count() -
1)
splittedCBGs = pacbpcol.find_fully_connected_subgraphs(
edges=cbg.node_count() - 1, max_missing_edges=0)
# convert to list of CBGs and do some transformations
cbgList = ListOfCodingBlockGraphs(splittedCBGs, input={}, crossdata={})
cbgList.remove_all_but_complete_cbgs()
cbgList.harvest_pacbps_from_pacbpcollection(dpcpacbpcol)
cbgList.remove_cbgs_without_omsr()
cbgList.update_edge_weights_by_minimal_spanning_range()
cbgList.order_list_by_attribute(order_by='total_weight', reversed=True)
############################################################################
if verbose:
for revcbg in cbgList:
print "revCBG:", revcbg
############################################################################
if not cbgList:
# no CBG on the reverse strand
return None
else:
# return the highest scoring CBG as a ReversecomlementCodingBlockGraph
return CodingBlockGraph2ReversecomlementCodingBlockGraph(
cbgList.codingblockgraphs[0])
# REMAP fastaheaders as ids to retrieve the Orfs after blast..
for orf in orfs[org].orfs: orf.fastaheader = str(orf.id)
fname = "%s_frameshiftcbg_%s.mfa" % (org,cbg.barcode())
writeMultiFasta(orfs[org].tofastadict(),fname)
multifastas[org] = fname
########################################################################
if verbose:
print "ORFS:", org, len(orfs[org].orfs),
print [ orf.id for orf in orfs[org].orfs ],
print [ str(orf) for orf in orfs[org].orfs ]
########################################################################
for orgQ,orgS in cbg.pairwisecrosscombinations_organism():
# create blastdb if it does not exist yet
if not blastdbs.has_key(orgS):
formatdb(fname=multifastas[orgS])
blastdbs[orgS] = multifastas[orgS]
for orfQ in orfs[orgQ].orfs:
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,orfQ.protein_sequence,
dbname="./"+blastdbs[orgS])
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# obtain coordinates from sbjct orf identifier
orfid = alignment.title.replace(">","").split(" ")[0].replace("_","")
orfS = orfs[orgS].get_orf_by_id(int(orfid))
nodeQ = ( orgQ, orfQ.id )
nodeS = ( orgS, orfS.id )
def blastanalysescbgjunction(gsg,prevCBG,nextCBG,
omit_cbg_orfs = False,
omit_non_cbg_orfs = False,
extra_blastp_params=CBG_JUNCTION_BLAST2PACBPCOL_EXTRA_BLASTP_PARAMS,
omsr_2_mask_aa_length_correction=CBG_JUNCTION_BLAST2PACBPCOL_OMSR_2_AA_MASK,
verbose=False):
"""
"""
############################################################
if verbose:
stw = StopWatch('blastanalysescbgjunction')
stw.start()
############################################################
orfs = {}
if not omit_cbg_orfs:
# gather Orfs from prevCBG and nextCBG
for org,orflist, in prevCBG.get_orfs_of_graph().iteritems():
orf = orflist[0]
orfs[(org,orf.id)] = orf
for org,orflist, in nextCBG.get_orfs_of_graph().iteritems():
orf = orflist[0]
orfs[(org,orf.id)] = orf
############################################################
if verbose:
print stw.lap(), "orfs (1):",len(orfs)
print _format_orf_nodes_to_string(orfs.keys())
############################################################
# create masked fasta database in a dict
fastadbmfa = parseFasta(
create_hmmdb_for_neighbouring_cbgs(
gsg.input,prevCBG,nextCBG,
omsr_2_mask_aa_length_correction=omsr_2_mask_aa_length_correction,
).split("\n")
)
############################################################
if verbose: print stw.lap(), "fasta db (1):",len(fastadbmfa)
############################################################
# remove ORFs that do not belong to prevCBG and nextCBG,
# or that DO belong to prevCBG and nextCBG, or neither
fastaheaders = fastadbmfa.keys()
for header in fastaheaders:
org,orfid = header.split("_orf_")
orfid = int(orfid)
node = (org,orfid)
# check for the omit_non_cbg_orfs criterion
add_orf = False
if omit_non_cbg_orfs:
if node not in orfs:
del(fastadbmfa[header])
else:
add_orf = True
# check for the omit_cbg_orfs criterion
if omit_cbg_orfs and node in orfs:
del(fastadbmfa[header])
if add_orf:
# get this Orf and add to orfs
orfs[node] = gsg.input[org]['orfs'].get_orf_by_id(orfid)
############################################################
if verbose:
print stw.lap(), "fasta db (2):",len(fastadbmfa)
print _format_fastadbmfa_nodes_to_string(fastadbmfa.keys())
############################################################
############################################################
if verbose:
print stw.lap(), "orfs (2):",len(orfs)
print _format_orf_nodes_to_string(orfs.keys())
############################################################
# no query/sbjct range left at all
if not fastadbmfa: return []
# check if all organisms are still covered
orgSet = Set([ k.split("_orf_")[0] for k in fastadbmfa.keys()])
if orgSet.symmetric_difference(gsg.organism_set()):
return []
# create !single! fasta database
fastadbname = prevCBG.barcode()+"_"+nextCBG.barcode()+".mfa"
writeMultiFasta(fastadbmfa,fastadbname)
formatdb(fname=fastadbname)
# remap the identifiers of the orf objects i.o.t....
multifastas = {}
blastdbs = {}
pacbpcol = PacbpCollectionGraph()
dpcpacbpcol = PacbpCollectionGraph() # ``deepcopied`` variant for pacbps
############################################################
if verbose: print stw.lap(), "blastp starting"
############################################################
for orgQ,orgS in prevCBG.pairwisecrosscombinations_organism():
for nodeQ,orfQ in orfs.iteritems():
# only blast the (masked) Orfs of orgQ
if prevCBG.organism_by_node(nodeQ) != orgQ: continue
# get the masked protein sequence of this orfObj
header = orgQ+"_orf_"+str(orfQ.id)
# check if key exists in fastadbmfa. In a case where
# an Orf is masked out completely, it is absent here!
if not fastadbmfa.has_key(header): continue
protseq = fastadbmfa[orgQ+"_orf_"+str(orfQ.id)]
# run blast_seqs2db
blastrec = blastall_seq2db(orfQ.id,protseq,fastadbname,
extra_blastp_params=extra_blastp_params)
# omit empty blast records
if len(blastrec.alignments) == 0: continue
for alignment in blastrec.alignments:
# get sbjct Org and Orf identifiers
_orgS,_orfSid = alignment.title.replace(">","").split("_orf_")
if _orgS != orgS: continue
nodeS = (_orgS,int(_orfSid))
orfS = orfs[nodeS]
# take only the *best* HSP (highest scoring first one)
hsp = alignment.hsps[0]
# correct to absolute positions
hsp.query_start = hsp.query_start + orfQ.protein_startPY
hsp.sbjct_start = hsp.sbjct_start + orfS.protein_startPY
# initialize the PacbP
pacbporf = pacb.conversion.pacbp2pacbporf(
pacb.PacbP(blastp_hsp=hsp),orfQ,orfS)
################################################################
if verbose:
print pacbporf, orgQ,orgS, orfQ
print pacbporf.query
print pacbporf.match
print pacbporf.sbjct
################################################################
# create nodes; ( Organism Identifier, Orf Identifier )
nodeQ = ( orgQ, orfQ.id )
nodeS = ( orgS, orfS.id )
uqkey = pacbporf.construct_unique_key(nodeQ,nodeS)
if not nodeQ in pacbpcol.get_nodes(): pacbpcol.add_node(nodeQ)
if not nodeS in pacbpcol.get_nodes(): pacbpcol.add_node(nodeS)
pacbpcol.add_edge(nodeQ,nodeS,wt=pacbporf.bitscore)
# store to dpcpacbpcol -> pacbpcol is broken in pieces lateron!
dpcpacbpcol.pacbps[(uqkey,nodeQ,nodeS)] = pacbporf
############################################################
if verbose: print stw.lap(), "blastp done"
############################################################
# file cleanup
_file_cleanup(multifastas.values())
_file_cleanup(["formatdb.log"])
_file_cleanup([ fname+".*" for fname in blastdbs.values()])
# check if all Organism/Gene identifiers are covered in PacbPs
if not pacbpcol.organism_set_size() == gsg.organism_set_size():
return []
# ``deepcopy`` PacbPcollection pacbpcol to dpcpacbpcol
# In dpcpacbpcol the actual PacbPORFs are stores & kept,
# whereas pacbpcol itself is splitted in CBGs (which
# function does not yet (!?) take the actual pacbps into account)
dpcpacbpcol.add_nodes( pacbpcol.get_nodes() )
for (uqkey,nodeQ,nodeS) in dpcpacbpcol.pacbps.keys():
(bitscore,length,orfQid,orfSid) = uqkey
dpcpacbpcol.add_edge(nodeQ,nodeS,wt=bitscore)
################################################################
if verbose:
print pacbpcol
print "PCG bitscores:",
print [ p.bitscore for p in dpcpacbpcol.pacbps.values() ]
