def to_biopython(self, qualifiers: Dict[str, Any] = None) -> List[SeqFeature]:
""" Converts this feature into one or more SeqFeature instances.
Subclasses must manage their own attributes and potential extra
features.
"""
feature = SeqFeature(self.location, type=self.type)
quals = self._qualifiers.copy()
notes = self._qualifiers.get("note", [])
assert notes is not None
notes.extend(self.notes)
if qualifiers:
notes += qualifiers.pop("note", [])
quals.update(qualifiers)
if notes:
# sorting helps with consistency and comparison testing
quals["note"] = sorted(notes)
if self.created_by_antismash:
quals["tool"] = ["antismash"]
if self._original_codon_start is not None:
start = int(self._original_codon_start)
quals["codon_start"] = [str(start + 1)]
# adjust location back if neccessary
if self.location.strand == -1:
start *= -1
if self._original_codon_start != 0:
feature.location = _adjust_location_by_offset(feature.location, -start)
# sorted here to match the behaviour of biopython
for key, val in sorted(quals.items()):
feature.qualifiers[key] = val
assert isinstance(feature.qualifiers, dict)
return [feature]
def _track(track_level):
track = diagram.new_track(track_level, greytrack=False)
feature_set = track.new_set()
for name, it in zip(names, intervals):
feat = SeqFeature(FeatureLocation(*it, strand=1))
feature_set.add_feature(feat,
name=name,
label=True,
label_angle=90)
for i, feat in enumerate(record.features[:8]):
loc = feat.location
eta = 4.8045
feat.location = FeatureLocation(int(loc.start / eta),
int(loc.end / eta),
strand=-1)
color = colors.blue if i % 2 == 0 else colors.lightblue
feature_set.add_feature(feat, color=color, label=True)
def gene2features(r, gene, gene2position, gene2product, start, end, gcode,
partialyes, verbose):
"""
"""
contig, CDSs, gffstrand, function, frames = gene2position[gene]
if gffstrand in ('1', '+'):
strand = +1
else:
strand = -1
CDSs.reverse()
'''#add stop codon if not partial seq
if strand==1 and CDSs[-1][1]+3 <= len(r.seq):
CDSs[-1][1] += 3
elif strand==-1 and CDSs[0][0]-3 > 0:
CDSs[0][0] -= 3'''
cdsloc, mrnaloc = get_locations(CDSs, start, end, strand)
#add gene
geneid = gene #".".join(gene.split('.')[:-1])
#get product
product = "hypothetical protein"
if geneid in gene2product:
product = gene2product[geneid]
if gene.endswith('.t1'):
sf = SeqFeature(FeatureLocation(BeforePosition(start - 1),
AfterPosition(end)),
strand=strand,
type='gene',
id=geneid)
sf.qualifiers = {
"locus_tag": geneid,
"gene": geneid,
"product": product
}
r.features.append(sf)
#get mRNA sf
sf = SeqFeature(mrnaloc, type='mRNA', id=gene)
sf.qualifiers = {
"locus_tag": geneid,
"gene": geneid,
"product": product
} #"protein_id": gene
r.features.append(sf)
#get CDS sf
sf = SeqFeature(cdsloc, type='CDS', id=gene)
#get translation
seq = sf.extract(r.seq)
aa = str(seq.translate(table=gcode))
#solve non-triplets issue
if len(seq) % 3:
if strand == 1:
end -= len(seq) % 3
else:
start += len(seq) % 3
##check for partial sequence - no M as first or no * as last aa
partial = 0
#both ends partial
if aa[0] != "M" and aa[-1] != "*":
partial = 1
sf.location = FeatureLocation(BeforePosition(start - 1),
AfterPosition(end))
#left end partial
elif aa[0] != "M" and strand == 1 or aa[-1] != "*" and strand == -1:
partial = 1
sf.location = FeatureLocation(BeforePosition(start - 1), end)
#right end partial
elif aa[-1] != "*" and strand == 1 or aa[0] != "M" and strand == -1:
partial = 1
sf.location = FeatureLocation(start - 1, AfterPosition(end))
#strip stop codon
aa = aa.strip("*")
#replace internal stop codons by X
if "*" in aa:
if verbose:
sys.stderr.write("[Warning] Stop codon(s) in: %s. Skipped!\n" %
gene)
return r
#aa = aa.replace("*","X")
sf.qualifiers = {
'transl_table': gcode,
"locus_tag": geneid,
"gene": geneid,
"product": product,
"translation": aa
} #"protein_id": gene,
if function:
sf.qualifiers['note'] = function
#inform about partial entries
if partial:
#skip if not partial are allowed
if not partialyes:
return r
if aa[0] != "M":
sf.qualifiers['codon_start'] = 1
sf.qualifiers['product'] += ", partial cds"
if verbose:
sys.stderr.write("[Warning] Partial sequence: %s\n" % (gene, ))
#sys.stderr.write("[Warning] Partial sequence: %s %s\n" % (gene,sf))
#add to features
r.features.append(sf)
return r
placeholder = SeqRecord(Seq("cgctatgcgaacaaaattgaactggaacgc", alphabet=IUPAC.unambiguous_dna), name=destination)
if args.vector:
base, ext = os.path.splitext(os.path.basename(args.vector))
output_filename = base + "_" + destination + ext
naive_construct, objectives, constraints = load_template(args.vector, placeholder, destination)
else:
output_filename = destination + ".gb"
objectives = []
constraints = []
naive_construct = placeholder
whole_seq_feat = SeqFeature()
whole_seq_feat.type = "misc_feature"
whole_seq_feat.qualifiers['label'] = [destination]
whole_seq_feat.location = FeatureLocation(0,len(placeholder),strand=1)
naive_construct.features.append(whole_seq_feat)
dest_feat = find_annotation(naive_construct, placeholder.name)
dest_loc = Location.from_biopython_location(dest_feat.location)
user_objectives, user_constraints = load_user_options(args, dest_loc)
objectives += user_objectives
constraints += user_constraints
problem = DnaOptimizationProblem(str(naive_construct.seq), constraints=constraints, objectives=objectives)
def agrupar_sitios():
regiones = list(
GFF.parse("/data/organismos/ILEX_PARA2/regulation/ncbi_IP4.gff3.reg"))
ids = 1
groups = {}
for c in tqdm(regiones):
groups[c.id] = []
for strand in [1, -1]:
group = SeqFeature(id=c.features[0],
type="grouped_transcription_regulatory_region",
location=c.features[0].location)
group.sub_features = []
fs = sorted([f for f in c.features if f.strand == strand],
key=lambda x: x.location.start)
if not fs:
continue
group.sub_features += [fs[0]]
for f in fs[1:]:
end = max([x.location.end for x in group.sub_features])
if ((abs(f.location.start - end) < 1500)
or (set(range(f.location.start, f.location.end)) & set(
range(group.sub_features[-1].location.start,
group.sub_features[-1].location.end)))):
group.sub_features.append(f)
else:
group.qualifiers = {
"description":
"_".join(
sorted(
set([
x.qualifiers["description"][0].split(
" regulatory region")[0]
for x in group.sub_features
]))),
"ID": ["ILEXPARARR" + str(ids)]
}
ids += 1
group.location = FeatureLocation(
start=min(
[x.location.start for x in group.sub_features]),
end=max([x.location.end for x in group.sub_features]),
strand=f.location.strand)
assert group.location.start < group.location.end
if (group.location.end - group.location.start) > 5000:
print(group.qualifiers["ID"])
groups[c.id].append(group)
group = SeqFeature(
id=c.features[0],
type="grouped_transcription_regulatory_region",
location=f.location)
group.sub_features = [f]
if group:
group.qualifiers = {
"description":
"_".join(
sorted(
set([
x.qualifiers["description"][0].split(
" binding site")[0]
for x in group.sub_features
]))),
"ID": ["ILEXPARARR" + str(ids)]
}
ids += 1
group.location = FeatureLocation(
start=min([x.location.start for x in group.sub_features]),
end=max([x.location.end for x in group.sub_features]),
strand=f.location.strand)
assert group.location.start < group.location.end
if (group.location.end - group.location.start) > 5000:
print(group.qualifiers["ID"])
groups[c.id].append(group)
# for _, v in groups.items():
# for x in v:
# x.sub_features = []
records = [
SeqRecord(id=k, name="", description="", seq=Seq(""), features=v)
for k, v in groups.items()
]
GFF.write(tqdm(records),
open("/data/organismos/ILEX_PARA2/regulation/grouped.gff", "w"))
def gene2features(r, gene, gene2position, gene2product, start, end, gcode, partialyes, verbose):
"""
"""
contig, CDSs, gffstrand, function, frames = gene2position[gene]
if gffstrand in ('1','+'):
strand = +1
else:
strand = -1
CDSs.reverse()
'''#add stop codon if not partial seq
if strand==1 and CDSs[-1][1]+3 <= len(r.seq):
CDSs[-1][1] += 3
elif strand==-1 and CDSs[0][0]-3 > 0:
CDSs[0][0] -= 3'''
cdsloc, mrnaloc = get_locations(CDSs, start, end, strand)
#add gene
geneid = gene #".".join(gene.split('.')[:-1])
#get product
product = "hypothetical protein"
if geneid in gene2product:
product = gene2product[geneid]
if gene.endswith('.t1'):
sf = SeqFeature(FeatureLocation(BeforePosition(start-1),AfterPosition(end)), strand=strand, type='gene', id=geneid)
sf.qualifiers={"locus_tag": geneid, "gene": geneid, "product": product}
r.features.append(sf)
#get mRNA sf
sf = SeqFeature(mrnaloc, type='mRNA', id=gene)
sf.qualifiers={"locus_tag": geneid, "gene": geneid, "product": product} #"protein_id": gene
r.features.append(sf)
#get CDS sf
sf = SeqFeature(cdsloc, type='CDS', id=gene)
#get translation
seq = sf.extract(r.seq)
aa = str(seq.translate(table=gcode))
#solve non-triplets issue
if len(seq) % 3:
if strand==1:
end -= len(seq) % 3
else:
start += len(seq) % 3
##check for partial sequence - no M as first or no * as last aa
partial = 0
#both ends partial
if aa[0]!="M" and aa[-1]!="*":
partial = 1
sf.location = FeatureLocation(BeforePosition(start-1),AfterPosition(end))
#left end partial
elif aa[0]!="M" and strand==1 or aa[-1]!="*" and strand==-1:
partial = 1
sf.location = FeatureLocation(BeforePosition(start-1),end)
#right end partial
elif aa[-1]!="*" and strand==1 or aa[0]!="M" and strand==-1:
partial = 1
sf.location = FeatureLocation(start-1,AfterPosition(end))
#strip stop codon
aa = aa.strip("*")
#replace internal stop codons by X
if "*" in aa:
if verbose:
sys.stderr.write("[Warning] Stop codon(s) in: %s. Skipped!\n" % gene)
return r
#aa = aa.replace("*","X")
sf.qualifiers = {'transl_table': gcode, "locus_tag": geneid, "gene": geneid, "product": product, "translation": aa} #"protein_id": gene,
if function:
sf.qualifiers['note'] = function
#inform about partial entries
if partial:
#skip if not partial are allowed
if not partialyes:
return r
if aa[0]!="M":
sf.qualifiers['codon_start'] = 1
sf.qualifiers['product'] += ", partial cds"
if verbose:
sys.stderr.write("[Warning] Partial sequence: %s\n" % (gene,))
#sys.stderr.write("[Warning] Partial sequence: %s %s\n" % (gene,sf))
#add to features
r.features.append(sf)
return r
def correct(_gff, _genome):
"""
:param _gff: gff path
:param _genome: fasta path
:return:
"""
_seqs = SeqIO.to_dict(SeqIO.parse(_genome, 'fasta'))
_gff = [_ for _ in GFF.parse(_gff, base_dict=_seqs)]
correct_list = []
gene_error_dict = defaultdict(list)
for scaffold in _gff:
correct_scaffold = SeqRecord(seq="", id=scaffold.id, name=scaffold.name, description=scaffold.description)
for gene in scaffold.features:
correct_gene = SeqFeature(location=gene.location,
type='gene',
strand=gene.strand,
id=gene.id,
qualifiers={'ID': [gene.id]})
correct_gene.sub_features = []
error_dict = defaultdict(list)
for mRNA in gene.sub_features:
try:
get_cds(mRNA, scaffold)
correct_gene.sub_features.append(mRNA)
except TranslationError as e:
try:
if e.args[0].startswith("First codon"):
_tmp_mrna = correct_start_codon(mRNA, scaffold)
get_cds(_tmp_mrna, scaffold)
correct_gene.sub_features.append(_tmp_mrna)
error_dict.setdefault('corrected', []).append(mRNA.id)
elif e.args[0].startswith('The phase of first CDS is not 0'):
# the translation was checked in function
_tmp_mrna = correct_phase(mRNA, scaffold)
correct_gene.sub_features.append(_tmp_mrna)
error_dict.setdefault('corrected', []).append(mRNA.id)
elif e.args[0].endswith("is not a stop codon"):
_tmp_mrna = correct_stop_codon(mRNA, scaffold)
get_cds(_tmp_mrna, scaffold)
correct_gene.sub_features.append(_tmp_mrna)
error_dict.setdefault('corrected', []).append(mRNA.id)
# can not handle for now
elif e.args[0] == "Extra in frame stop codon found.":
error_dict.setdefault('internal', []).append(mRNA.id)
elif e.args[0].endswith("is not a multiple of three"):
error_dict.setdefault('three', []).append(mRNA.id)
except TranslationError as e2:
if e2.args[0].startswith('These mRNAs need another round correction'):
correct_gene.sub_features.append(e2.args[1])
error_dict.setdefault('phase', []).append(mRNA.id)
# for second round
elif e2.args[0] == "Extra in frame stop codon found":
error_dict.setdefault('internal', []).append(mRNA.id)
elif e2.args[0].startswith('First codon'):
error_dict.setdefault('first2', []).append(mRNA.id)
elif e2.args[0].endswith("is not a stop codon"):
error_dict.setdefault('final', []).append(mRNA.id)
elif e2.args[0].endswith("is not a multiple of three"):
error_dict.setdefault('three', []).append(mRNA.id)
except Exception as e:
print(e)
print(mRNA.id)
# handle mRNA and gene relationship
if not correct_gene.sub_features:
# Raise error for genes whose all mRNAs have error.
for _key, value in error_dict.items():
_tmp_error = [gene.id + ' ' + _ for _ in value]
gene_error_dict[_key] += _tmp_error
else:
# check boundary conflict between gene and mRNA.
gene_start, gene_end = gene.location.start, gene.location.end
for mRNA in correct_gene.sub_features:
if mRNA.location.start < correct_gene.location.start:
gene_start = mRNA.location.start
if mRNA.location.end > correct_gene.location.end:
gene_end = mRNA.location.end
correct_gene.location = FeatureLocation(gene_start, gene_end, strand=correct_gene.strand)
correct_scaffold.features.append(correct_gene)
correct_list.append(correct_scaffold)
# tidy correct list
return correct_list, gene_error_dict
'label': 'B0015 Double Terminator',
'note': ['color: #ff8eff', '"iGEM Part: BBa_B0015"']
}
# merge Lux pL promoter
r0063 = next(get_features('R0063'), None)
if r0063 is not None:
luxpl = next(get_features('Lux pL promoter'))
luxpl.location = r0063.location
gb_archive.features.remove(r0063)
# add LVA ssrA tag
ssra_match = SSRA_TAG.search(gb_archive.seq)
if ssra_match is not None:
ssra = SeqFeature(type="CDS")
ssra.location = FeatureLocation(*ssra_match.span(), strand=1)
ssra.qualifiers = {
"label": ["ssrA tag (LVA)"],
"product": [
"C-terminal peptide that mediates degradation in bacteria through the ClpXP and ClpAP proteases (McGinness et al., 2006)"
],
"translation":
"AANDENYALVA",
"note": [
"mutant LVA variant that confers accelerated degradation under some conditions (Andersen et al., 1998)",
"color: #cc99b2",
],
}
gb_archive.features.append(ssra)
# Replace E0040m with well annotated GFP
print('\n---Exercise 5---')
id = "PAX-6.5"
format = "fasta"
record = SeqIO.read(open(id + "." + format), format)
print("Record:\n", record)
record.seq.alphabet = IUPAC.unambiguous_dna
print("\nAlphabet altered to IUPAC.unambiguous_dna !!!")
accNb = record.id.split("|")[3]
print("Access number: ", accNb)
record.name = accNb
record.id = accNb
print("record.name and record.id have been altered !!!")
feature = SeqFeature()
feature.type = "gene"
feature.location = FeatureLocation(18, 200)
feature.strand = -1
record.features.append(feature)
print("record.features: ", record.features)
print("\nRecord:\n", record)
count = SeqIO.write(record, open(id + ".gb", "w"), "genbank")
print("Converted %i records" % count)
if 6 in _RunExercise:
print('\n---ORF---')
mail = ''
id = "NC_009926"
db = "nuccore"
format = "fasta"
