def BEDIterator(handle):
"""Generator function to iterate over Fasta records (as SeqRecord objects).
handle - input file
If this is not given, then the entire title line will be used
as the description, and the first word as the id and name.
Note that use of title2ids matches that of Bio.Fasta.SequenceParser
but the defaults are slightly different.
"""
line_no = 0
#Skip any text before the first record (e.g. blank lines, comments)
while True :
line_no += 1
line = handle.readline().strip()
if not line:
return
if line[0] == "#" or len(line) == 0:
continue
try:
ref,source,type,start,end,score,strand,frame,attributes = \
line.split("\t")
except:
raise FormatError, "Problem with line %d in %s. Line was\n%s" %\
(line_no,handle.name,line)
attr_pairs = attributes.strip(';').split(";")
attr_dict = dict(map(lambda x: tuple(x.split("=")), attr_pairs))
result = SeqFeature(location=FeatureLocation(int(start),int(end)),
type=type,strand=_gff3_strand_to_numeric[strand],ref=ref,ref_db=source)
result.id = attr_dict.get("ID",None)
result.name = attr_dict.get("Name",None)
result.attributes = attr_dict # not an official property of SeqFeature.
yield result
def ncrna_gene(self, ncrna):
"""Create a gene for ncRNAs"""
gene = SeqFeature(ncrna.location, type="ncRNA_gene")
gene.qualifiers["source"] = ncrna.qualifiers["source"]
gene.sub_features = [ncrna]
gene.id = ncrna.id
return gene
def cds_gene(self, cds):
"""Create a gene for a lone CDS"""
# Create a transcript, add the CDS
transcript = SeqFeature(cds.location, type="mRNA")
transcript.qualifiers["source"] = cds.qualifiers["source"]
transcript.sub_features = [cds]
# Add an exon too
exon = SeqFeature(cds.location, type="exon")
exon.qualifiers["source"] = cds.qualifiers["source"]
transcript.sub_features.append(exon)
# Create a gene, add the transcript
gene = SeqFeature(cds.location, type="gene")
gene.qualifiers["source"] = cds.qualifiers["source"]
gene.sub_features = [transcript]
gene.id = self.generate_stable_id()
return gene
def gbk2gff(genbank_path, new_gff_path, species_id):
print('Start change', os.path.basename(new_gff_path))
records_list = []
genome = SeqIO.read(genbank_path, "genbank")
remove_none_location(genome)
genome.features.sort(key=lambda x: x.location.start)
gene_count = 0
IR_count = 0
for ele in genome.features:
if ele.type == 'gene':
if ele.qualifiers['gene'][0] == 'rps12':
continue
gene_count += 1
ele.id = species_id + '%03d' % gene_count
for child_feature in genome[ele.location.start:ele.location.
end].features:
fix_location(child_feature, ele.location.start)
if child_feature.type != 'gene' and \
child_feature.location.start == ele.location.start and \
child_feature.location.end == ele.location.end:
child_feature.type = 'mRNA' if child_feature.type == 'CDS' else child_feature.type
if child_feature.qualifiers['gene'][0] == ele.qualifiers[
'gene'][0]:
# This module for protein coding gene CDS region
if child_feature.type == 'mRNA':
gene_attributes = [
'ID=' + ele.id,
'Name=' + ele.qualifiers['gene'][0],
'gene_biotype=protein_coding'
]
records_list.append(
get_record(ele, gene_attributes))
cds_count = 0
for cds in reversed(child_feature.location.parts):
cds_count += 1
cds_feature = SeqFeature(
cds,
type='CDS',
qualifiers={
'codon_start':
child_feature.qualifiers['codon_start']
[0]
})
cds_feature.id = 'cds_' + species_id + '%03d' % gene_count + '_' + '%d' % cds_count
cds_attributes = [
'ID=' + cds_feature.id, 'Parent=' + ele.id,
'product=' +
child_feature.qualifiers['product'][0]
]
records_list.append(
get_record(cds_feature, cds_attributes))
# This module for rRNA and tRNA exon
else:
# gene
gene_attributes = [
'ID=' + ele.id,
'Name=' + ele.qualifiers['gene'][0],
'gene_biotype=' + child_feature.type
]
records_list.append(
get_record(ele, gene_attributes))
# rna
child_feature.id = 'rna_' + species_id + '%03d' % gene_count
child_attributes = [
'ID=' + child_feature.id, 'Parent=' + ele.id,
'product=' +
child_feature.qualifiers['product'][0]
]
records_list.append(
get_record(child_feature, child_attributes))
exon_list = []
exon_count = 0
# exon
for exon in reversed(child_feature.location.parts):
exon_count += 1
exon_feature = SeqFeature(exon, type='exon')
exon_feature.id = 'exon_' + species_id + '%03d' % gene_count + '_' + '%d' % exon_count
exon_attributes = [
'ID=' + exon_feature.id,
'Parent=' + child_feature.id
]
exon_list.append(
get_record(exon_feature, exon_attributes))
if exon_count > 1:
records_list += exon_list
elif ele.type == 'repeat_region':
IR_count += 1
gene_attributes = [
'ID=IR' + str(IR_count), 'note=Inverted repeats'
]
records_list.append(get_record(ele, gene_attributes))
records_dict = {index: record for index, record in enumerate(records_list)}
result_gff = pd.DataFrame.from_dict(records_dict, 'index')
result_gff['seqid'] = genome.id
result_gff['score'] = '.'
result_gff['source'] = 'PGA'
result_gff = result_gff[[
"seqid", "source", "type", "start", "end", "score", "strand", "phase",
"attributes"
]]
result_gff.to_csv(new_gff_path,
sep='\t',
header=False,
index=False,
encoding='utf8')
return genome.seq
# st and en are unmodified from the blast file # they can be backwards # original row as of nov23 read #feature = SeqFeature(FeatureLocation(st-1,en), strand=framepart2,type="repeathit") # start location should not be modified by -1 in this case # changed Featurelocation start, older line: #feature = SeqFeature(FeatureLocation(st,en), strand=framepart2,type="repeathit") # Genbank magic adds one to start position? feature = SeqFeature(FeatureLocation(st-1,en), strand=framepart2,type="repeathit") #feature.id=rename #feature.qualifiers["hit"]=rename feature.id=isname feature.qualifiers["hit"]=isname feature.qualifiers["sequence_length"]=str(len(contigseq[myhsp.sbjct_start-1:myhsp.sbjct_end])) # feature.qualifiers["score"]=str(myhsp.score) if myhsp.score>bestscorehsp.score: bestscorehsp=myhsp if myhsp.expect<bestexphsp.expect: bestexphsp=myhsp # hit length is disance from hits start plus hit end feature.qualifiers["hitlength"]=str(1+max(st,en)-min(st,en)) # feature.qualifiers["expect"]=str(myhsp.expect) feature.qualifiers["query_start"]=str(myhsp.query_start)
for feature in feature_lambda(record.features, feature_test_true, {}):
if feature.type in args.changeList:
#if "Parent" in feature.qualifiers.keys():
#endOfChain = False
#while endOfChain == False:
# parentFeat = record.features(feature.qualifiers["Parent"][0])
#for x in range(0, len(args.changeList)):
#feature.qualifiers["Parent"] = []
newChain = [feature]
tempParent = ""
if "Parent" in feature.qualifiers.keys():
tempParent = feature.qualifiers["Parent"][0]
for x in range(0, len(args.changeTo)):
tempFeat = SeqFeature(location=feature.location)
tempFeat.type = args.changeTo[len(args.changeTo) - 1 - x]
tempFeat.id = feature.id + "_p" + str(
len(args.changeTo) - x)
tempFeat.ref_db = feature.ref_db
tempFeat.ref = feature.ref
#tempFeat.sub_features.append(newChain[x])
if "Parent" in newChain[x].qualifiers.keys():
newChain[x].qualifiers["Parent"][
0] = feature.id + "_p" + str(
len(args.changeTo) - x)
else:
newChain[x].qualifiers["Parent"] = [
feature.id + "_p" + str(len(args.changeTo) - x)
]
tempFeat.qualifiers["ID"] = [tempFeat.id]
if "Name" in newChain[x].qualifiers.keys():
tempFeat.qualifiers["Name"] = [
feature.qualifiers["Name"][0] + "_p" +
