def create_gene_utrs(gene_gff_list):
"""
Create UTR tracks for an (annotated) gene
@type gene_gff_list: list
@param gene_gff_list: list with gff tuples of the (annotated) gene
@rtype utrs: list
@return utrs: list with gff tuples of the UTR tracks
@attention: requires global variables GFF_CDS_FMETHOD, GFF_EXON_FMETHOD
@attention: requires global variables GFF_UTR5_FSOURCE, GFF_UTR5_FMETHOD
@attention: requires global variables GFF_UTR3_FSOURCE, GFF_UTR3_FMETHOD
"""
# make sets of unigene coordinates
cdscoords = gffs2coordset(gene_gff_list,fmethod=[GFF_CDS_FMETHOD])
exoncoords = gffs2coordset(gene_gff_list,fmethod=[GFF_EXON_FMETHOD])
# return list with UTR tracks
utrs = []
# create a list with 5'UTR coordinates
if cdscoords and exoncoords:
utr5p_coords = []
utr3p_coords = []
# find start codon in cdscoords: min()
for coord in range( min(exoncoords), min(cdscoords) ):
if coord in exoncoords:
utr5p_coords.append(coord)
# find stop codon in exoncoords: max()
if max(cdscoords)+3 != max(exoncoords):
# check if exon-end != cds-end+3 -> only a stop codon
for coord in range( max(cdscoords)+1, max(exoncoords)+1 ):
if coord in exoncoords:
utr3p_coords.append(coord)
if utr5p_coords or utr3p_coords:
# get list with coding exons for track backbone
cexons = filtergffs4fmethod(gene_gff_list,fmethod=GFF_CDS_FMETHOD)
# create 5'UTRs
gfftrack = list( cexons[0] )
gfftrack[1] = GFF_UTR5_FSOURCE
gfftrack[2] = GFF_UTR5_FMETHOD
utrs.extend( coordset2gfftracks(utr5p_coords,gfftrack))
# create 3'UTRs
gfftrack = list( cexons[0] )
gfftrack[1] = GFF_UTR3_FSOURCE
gfftrack[2] = GFF_UTR3_FMETHOD
utrs.extend( coordset2gfftracks(utr3p_coords,gfftrack))
# return the utr tracks
return utrs
def correct_unigene_for_utrs(
unigene_gff_list,
start_codon_gff=(),
stop_codon_gff=(),
minimal_likely_tss_pssm_score=3.0,
shift_tss_pssm_score_ratio=4.0,
dnaseqfname=None,
verbose=False,
):
"""
Check if unigene contains evidence for non-coding UTRs and if so, correct
@type unigene_gff_list: list
@param unigene_gff_list: list with uncorrected unigene gff tuples
@type start_codon_gff: tuple
@param start_codon_gff: tuple representing the (annotated) protein's start codon
@type stop_codon_gff: tuple
@param stop_codon_gff: tuple representing the (annotated) protein's stop codon
@type dnaseqfname: string (or None)
@param dnaseqfname: filename of DNA sequence corresponding to the unigene's GFF
@type minimal_likely_tss_pssm_score: float
@param minimal_likely_tss_pssm_score: minimal (likely) PSSM score of the TSS
@type shift_tss_pssm_score_ratio: float
@param shift_tss_pssm_score_ratio: shift TSS downstream when ratio is exceeded
@type verbose: Boolean
@param verbose: print discrepancies to STDOUT (True) or not (False, default)
@rtype: list of (gff) tuples + typeofunigene string
@return: list with corrected gff tuples + string
@attention: Global variable GFF_UGEXON_FMETHOD is required for this function
@attention: Global variable GFF_UG3UTREXON_FMETHOD is required for this function
@attention: Global variable GFF_UG5UTREXON_FMETHOD is required for this function
"""
# return list with corrected unigene tracks
return_unigene_gff_list = []
start_codon_pos = None
stop_codon_pos = None
typeofunigene = None
# make sets of unigene coordinates
unigene_coordinate_set = gffs2coordset(unigene_gff_list, fmethod=[GFF_UGEXON_FMETHOD])
if dnaseqfname:
# print unigene structure annotation
unigeneexons = filtergffs4fmethod(unigene_gff_list, GFF_UGEXON_FMETHOD)
unigeneexons.sort()
# replace fasta header for correct recognition
# header,descr = parseSingleFastaHeaderFromFile(dnaseqfname)
header, dnaseq, descr = parseSingleFasta(open(dnaseqfname).readlines())
for i in range(0, len(unigeneexons)):
gff = list(unigeneexons[i])
gff[0] = header
# correct for negative coordinate. This can happen in case
# the unigene sticks out of the genelocus
if gff[3] <= 0:
gff[3] = 1
unigeneexons[i] = tuple(gff)
# run unigeneannotation command
command = "%s %s %s" % (PYTHON_PATH, EXECUTABLE_UNIGENEANNOTATION, dnaseqfname)
ci, co = os.popen2(command)
ci.write(gffs2txt(unigeneexons))
ci.close()
ugannotation = co.read().strip().split("\t")
co.close()
typeofunigene = ugannotation[0]
# abstract coordinates of start and stop codon
# from unigene annotation
try:
start_codon_pos = int(ugannotation[5])
except:
start_codon_pos = None
try:
stop_codon_pos = int(ugannotation[6])
except:
stop_codon_pos = None
################################################################
if verbose:
for track in unigene_gff_list:
print track
print ugannotation, start_codon_pos, stop_codon_pos
print "given ATG:", start_codon_gff
print "given TGA:", stop_codon_gff
################################################################
if start_codon_pos:
# check if the PythonRegex obtained Methionine is the most
# likely TSS. When a far better one is available -> shift
# the TSS downstream (5p->3p) to this better TSS.
startcodons = []
for gffpos in range(start_codon_pos, int(unigeneexons[0][4]), 3):
if dnaseq[gffpos - 1 : gffpos - 1 + 3].upper() == "ATG":
tssSta = gffpos - 1 - IC_TSS_PATTERN_OFFSET[0]
tssEnd = gffpos - 1 + 3 + IC_TSS_PATTERN_OFFSET[1]
tssSeq = dnaseq[tssSta:tssEnd]
tssSco = score_tss(tssSeq)
# print 'ATG', gffpos, "%1.2f" % tssSco
startcodons.append((tssSco, gffpos))
# check if there are >1 start codon posibilities
if len(startcodons) > 1 and startcodons[0][0] < minimal_likely_tss_pssm_score:
for score, gffpos in startcodons[1:]:
if (
score >= minimal_likely_tss_pssm_score
and abs(score / startcodons[0][0]) > shift_tss_pssm_score_ratio
):
start_codon_pos = gffpos
# print "TSS pos SHIFTED", startcodons[0][1], "->", gffpos
# break out after first shift; this is now *THE* TSS
break
elif start_codon_gff:
# unigene is a fragment or other transcript without
# likely ATG. Fortunately, ATG is applied from the given
# gene structure. Take this one.
start_codon_pos = int(start_codon_gff[3])
else:
# NO start_codon_pos available -> unigene fragment!
pass
elif start_codon_gff or stop_codon_gff:
typeofunigene = None # unknown -> no unigeneannotation
# No dna sequence is applied to verify the ATG/TGA
# positions of the unigene by unigene annotation.
# Abstract coordinates of start and/or stop codons
# from the given coordinates (from the gene's annotation)
if start_codon_gff:
start_codon_pos = int(start_codon_gff[3])
if stop_codon_gff:
stop_codon_pos = int(stop_codon_gff[4])
else:
typeofunigene = None # unknown -> no unigeneannotation
########################################################
if verbose:
print "NONE GIVEN seq/sta/end:", dnaseqfname
print "gff ATG:", start_codon_gff
print "gff TGA:", stop_codon_gff
########################################################
# no anchors applied in terms of start/stop sites
# TODO future update: find or predict the putative orf
# of this unigene. That specific functionallity should
# NOT be placed in this function!
# for the time being, just return the input gff list.
return unigene_gff_list, typeofunigene
# create an unigene stop codon track when in unigene_coordinate_set
if stop_codon_pos and stop_codon_pos in unigene_coordinate_set:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = "UGstop"
newgff[3] = stop_codon_pos - 2
newgff[4] = stop_codon_pos
return_unigene_gff_list.append(tuple(newgff))
# CORRECT the unigene_coordinate_set for 5p nucleotides
ignore_5p_coords = []
if (
start_codon_pos != None
and start_codon_pos in unigene_coordinate_set
and min(unigene_coordinate_set) < start_codon_pos
):
if verbose:
print "CREATE 5pUTR for ug:", typeofunigene
# yes, there is a 5p unigene alignment part
for coord in unigene_coordinate_set:
if coord < start_codon_pos:
# append to the ignore_5p_coords list
ignore_5p_coords.append(coord)
# remove from the unigene coord set
for coord in ignore_5p_coords:
unigene_coordinate_set.remove(coord)
# CORRECT the unigene_coordinate_set for 3p nucleotides
ignore_3p_coords = []
if (
stop_codon_pos != None
and stop_codon_pos in unigene_coordinate_set
and max(unigene_coordinate_set) > stop_codon_pos
):
if verbose:
print "CREATE 3pUTR for ug:", typeofunigene
# yes, there is a 3p unigene alignment part
for coord in unigene_coordinate_set:
if coord > stop_codon_pos:
# append to the ignore_5p_coords list
ignore_3p_coords.append(coord)
# remove from the unigene coord set
for coord in ignore_3p_coords:
unigene_coordinate_set.remove(coord)
#### remove the stop codon position too
###unigene_coordinate_set.remove(stop_codon_pos-2)
###unigene_coordinate_set.remove(stop_codon_pos-1)
###unigene_coordinate_set.remove(stop_codon_pos)
# make (new) UGExon tracks, corrected for UTRS, if needed
if not (ignore_5p_coords or ignore_3p_coords) and unigene_coordinate_set:
# no utrs available; just set the input to the output list
return_unigene_gff_list.extend(unigene_gff_list)
elif (ignore_5p_coords or ignore_3p_coords) and unigene_coordinate_set:
# create new gff tracks for unigene exons
unigene_exon_coords = list(unigene_coordinate_set)
unigene_exon_coords.sort()
track_coords = [[unigene_exon_coords[0]]]
for coord in unigene_exon_coords[1:]:
if coord == max(track_coords[-1]) + 1:
track_coords[-1].append(coord)
else:
track_coords.append([coord])
for track in track_coords:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[3] = min(track)
newgff[4] = max(track)
# and append to the new return unigene gff list
return_unigene_gff_list.append(tuple(newgff))
# make UTR5UGExon track if it exists
if ignore_5p_coords:
ignore_5p_coords.sort()
tracks = [[ignore_5p_coords[0]]]
for coord in ignore_5p_coords[1:]:
if coord == max(tracks[-1]) + 1:
tracks[-1].append(coord)
else:
tracks.append([coord])
# reverse tracks; if there are >1, inserting in the
# return list will guarantee the correct order
tracks.reverse()
for track in tracks:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = GFF_UG5UTREXON_FMETHOD
newgff[3] = min(track)
newgff[4] = max(track)
# and insert as the first the new return unigene gff list
return_unigene_gff_list.insert(0, tuple(newgff))
# make UTR3UGExon track
if ignore_3p_coords:
ignore_3p_coords.sort()
tracks = [[ignore_3p_coords[0]]]
for coord in ignore_3p_coords[1:]:
if coord == max(tracks[-1]) + 1:
tracks[-1].append(coord)
else:
tracks.append([coord])
for track in tracks:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = GFF_UG3UTREXON_FMETHOD
newgff[3] = min(track)
newgff[4] = max(track)
# and append to the new return unigene gff list
return_unigene_gff_list.append(tuple(newgff))
else:
# hmm... not really expected. There are UniGene tracks,
# but no UniGene exons are recognized. Probably a wrong setting
# applied for GFF_UGEXON_FMETHOD (not identical to the naming in
# the input gff.
pass
# order the unigene gff list (stop codon potentially on the front
return_unigene_gff_list = order_gff_list(return_unigene_gff_list)
################################################################
if verbose and (ignore_5p_coords or ignore_3p_coords):
for track in return_unigene_gff_list:
print track
################################################################
# done! return the new list
return return_unigene_gff_list, typeofunigene
def correct_unigene_for_utrs(unigene_gff_list,
start_codon_gff=(),
stop_codon_gff=(),
minimal_likely_tss_pssm_score=3.0,
shift_tss_pssm_score_ratio=4.0,
dnaseqfname=None,
verbose=False):
"""
Check if unigene contains evidence for non-coding UTRs and if so, correct
@type unigene_gff_list: list
@param unigene_gff_list: list with uncorrected unigene gff tuples
@type start_codon_gff: tuple
@param start_codon_gff: tuple representing the (annotated) protein's start codon
@type stop_codon_gff: tuple
@param stop_codon_gff: tuple representing the (annotated) protein's stop codon
@type dnaseqfname: string (or None)
@param dnaseqfname: filename of DNA sequence corresponding to the unigene's GFF
@type minimal_likely_tss_pssm_score: float
@param minimal_likely_tss_pssm_score: minimal (likely) PSSM score of the TSS
@type shift_tss_pssm_score_ratio: float
@param shift_tss_pssm_score_ratio: shift TSS downstream when ratio is exceeded
@type verbose: Boolean
@param verbose: print discrepancies to STDOUT (True) or not (False, default)
@rtype: list of (gff) tuples + typeofunigene string
@return: list with corrected gff tuples + string
@attention: Global variable GFF_UGEXON_FMETHOD is required for this function
@attention: Global variable GFF_UG3UTREXON_FMETHOD is required for this function
@attention: Global variable GFF_UG5UTREXON_FMETHOD is required for this function
"""
# return list with corrected unigene tracks
return_unigene_gff_list = []
start_codon_pos = None
stop_codon_pos = None
typeofunigene = None
# make sets of unigene coordinates
unigene_coordinate_set = gffs2coordset(unigene_gff_list,
fmethod=[GFF_UGEXON_FMETHOD])
if dnaseqfname:
# print unigene structure annotation
unigeneexons = filtergffs4fmethod(unigene_gff_list, GFF_UGEXON_FMETHOD)
unigeneexons.sort()
# replace fasta header for correct recognition
#header,descr = parseSingleFastaHeaderFromFile(dnaseqfname)
header, dnaseq, descr = parseSingleFasta(open(dnaseqfname).readlines())
for i in range(0, len(unigeneexons)):
gff = list(unigeneexons[i])
gff[0] = header
# correct for negative coordinate. This can happen in case
# the unigene sticks out of the genelocus
if gff[3] <= 0: gff[3] = 1
unigeneexons[i] = tuple(gff)
# run unigeneannotation command
command = "%s %s %s" % (PYTHON_PATH, EXECUTABLE_UNIGENEANNOTATION,
dnaseqfname)
ci, co = os.popen2(command)
ci.write(gffs2txt(unigeneexons))
ci.close()
ugannotation = co.read().strip().split("\t")
co.close()
typeofunigene = ugannotation[0]
# abstract coordinates of start and stop codon
# from unigene annotation
try:
start_codon_pos = int(ugannotation[5])
except:
start_codon_pos = None
try:
stop_codon_pos = int(ugannotation[6])
except:
stop_codon_pos = None
################################################################
if verbose:
for track in unigene_gff_list:
print track
print ugannotation, start_codon_pos, stop_codon_pos
print "given ATG:", start_codon_gff
print "given TGA:", stop_codon_gff
################################################################
if start_codon_pos:
# check if the PythonRegex obtained Methionine is the most
# likely TSS. When a far better one is available -> shift
# the TSS downstream (5p->3p) to this better TSS.
startcodons = []
for gffpos in range(start_codon_pos, int(unigeneexons[0][4]), 3):
if dnaseq[gffpos - 1:gffpos - 1 + 3].upper() == 'ATG':
tssSta = gffpos - 1 - IC_TSS_PATTERN_OFFSET[0]
tssEnd = gffpos - 1 + 3 + IC_TSS_PATTERN_OFFSET[1]
tssSeq = dnaseq[tssSta:tssEnd]
tssSco = score_tss(tssSeq)
#print 'ATG', gffpos, "%1.2f" % tssSco
startcodons.append((tssSco, gffpos))
# check if there are >1 start codon posibilities
if len(startcodons) > 1 and startcodons[0][0] <\
minimal_likely_tss_pssm_score:
for score, gffpos in startcodons[1:]:
if score >= minimal_likely_tss_pssm_score and\
abs( score / startcodons[0][0] ) > shift_tss_pssm_score_ratio:
start_codon_pos = gffpos
#print "TSS pos SHIFTED", startcodons[0][1], "->", gffpos
# break out after first shift; this is now *THE* TSS
break
elif start_codon_gff:
# unigene is a fragment or other transcript without
# likely ATG. Fortunately, ATG is applied from the given
# gene structure. Take this one.
start_codon_pos = int(start_codon_gff[3])
else:
# NO start_codon_pos available -> unigene fragment!
pass
elif start_codon_gff or stop_codon_gff:
typeofunigene = None # unknown -> no unigeneannotation
# No dna sequence is applied to verify the ATG/TGA
# positions of the unigene by unigene annotation.
# Abstract coordinates of start and/or stop codons
# from the given coordinates (from the gene's annotation)
if start_codon_gff:
start_codon_pos = int(start_codon_gff[3])
if stop_codon_gff:
stop_codon_pos = int(stop_codon_gff[4])
else:
typeofunigene = None # unknown -> no unigeneannotation
########################################################
if verbose:
print "NONE GIVEN seq/sta/end:", dnaseqfname
print "gff ATG:", start_codon_gff
print "gff TGA:", stop_codon_gff
########################################################
# no anchors applied in terms of start/stop sites
# TODO future update: find or predict the putative orf
# of this unigene. That specific functionallity should
# NOT be placed in this function!
# for the time being, just return the input gff list.
return unigene_gff_list, typeofunigene
# create an unigene stop codon track when in unigene_coordinate_set
if stop_codon_pos and stop_codon_pos in unigene_coordinate_set:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = 'UGstop'
newgff[3] = stop_codon_pos - 2
newgff[4] = stop_codon_pos
return_unigene_gff_list.append(tuple(newgff))
# CORRECT the unigene_coordinate_set for 5p nucleotides
ignore_5p_coords = []
if start_codon_pos != None and start_codon_pos in\
unigene_coordinate_set and min(unigene_coordinate_set) < start_codon_pos:
if verbose: print "CREATE 5pUTR for ug:", typeofunigene
# yes, there is a 5p unigene alignment part
for coord in unigene_coordinate_set:
if coord < start_codon_pos:
# append to the ignore_5p_coords list
ignore_5p_coords.append(coord)
# remove from the unigene coord set
for coord in ignore_5p_coords:
unigene_coordinate_set.remove(coord)
# CORRECT the unigene_coordinate_set for 3p nucleotides
ignore_3p_coords = []
if stop_codon_pos != None and stop_codon_pos in\
unigene_coordinate_set and max(unigene_coordinate_set) > stop_codon_pos:
if verbose: print "CREATE 3pUTR for ug:", typeofunigene
# yes, there is a 3p unigene alignment part
for coord in unigene_coordinate_set:
if coord > stop_codon_pos:
# append to the ignore_5p_coords list
ignore_3p_coords.append(coord)
# remove from the unigene coord set
for coord in ignore_3p_coords:
unigene_coordinate_set.remove(coord)
#### remove the stop codon position too
###unigene_coordinate_set.remove(stop_codon_pos-2)
###unigene_coordinate_set.remove(stop_codon_pos-1)
###unigene_coordinate_set.remove(stop_codon_pos)
# make (new) UGExon tracks, corrected for UTRS, if needed
if not (ignore_5p_coords or ignore_3p_coords) and unigene_coordinate_set:
# no utrs available; just set the input to the output list
return_unigene_gff_list.extend(unigene_gff_list)
elif (ignore_5p_coords or ignore_3p_coords) and unigene_coordinate_set:
# create new gff tracks for unigene exons
unigene_exon_coords = list(unigene_coordinate_set)
unigene_exon_coords.sort()
track_coords = [[unigene_exon_coords[0]]]
for coord in unigene_exon_coords[1:]:
if coord == max(track_coords[-1]) + 1:
track_coords[-1].append(coord)
else:
track_coords.append([coord])
for track in track_coords:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[3] = min(track)
newgff[4] = max(track)
# and append to the new return unigene gff list
return_unigene_gff_list.append(tuple(newgff))
# make UTR5UGExon track if it exists
if ignore_5p_coords:
ignore_5p_coords.sort()
tracks = [[ignore_5p_coords[0]]]
for coord in ignore_5p_coords[1:]:
if coord == max(tracks[-1]) + 1:
tracks[-1].append(coord)
else:
tracks.append([coord])
# reverse tracks; if there are >1, inserting in the
# return list will guarantee the correct order
tracks.reverse()
for track in tracks:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = GFF_UG5UTREXON_FMETHOD
newgff[3] = min(track)
newgff[4] = max(track)
# and insert as the first the new return unigene gff list
return_unigene_gff_list.insert(0, tuple(newgff))
# make UTR3UGExon track
if ignore_3p_coords:
ignore_3p_coords.sort()
tracks = [[ignore_3p_coords[0]]]
for coord in ignore_3p_coords[1:]:
if coord == max(tracks[-1]) + 1:
tracks[-1].append(coord)
else:
tracks.append([coord])
for track in tracks:
# make a deepcopy of the first unigene exon track and make a list of it
newgff = list(deepcopy(unigene_gff_list[0]))
# update the coordinates
newgff[2] = GFF_UG3UTREXON_FMETHOD
newgff[3] = min(track)
newgff[4] = max(track)
# and append to the new return unigene gff list
return_unigene_gff_list.append(tuple(newgff))
else:
# hmm... not really expected. There are UniGene tracks,
# but no UniGene exons are recognized. Probably a wrong setting
# applied for GFF_UGEXON_FMETHOD (not identical to the naming in
# the input gff.
pass
# order the unigene gff list (stop codon potentially on the front
return_unigene_gff_list = order_gff_list(return_unigene_gff_list)
################################################################
if verbose and (ignore_5p_coords or ignore_3p_coords):
for track in return_unigene_gff_list:
print track
################################################################
# done! return the new list
return return_unigene_gff_list, typeofunigene