def rebuild_references(annotations: Dict) -> Dict[str, List[Reference]]:
""" Rebuilds the SeqRecord 'references' annotation from JSON """
bases = annotations["references"]
refs = []
for ref in bases:
new_reference = Reference()
new_reference.__dict__ = ref
new_reference.location = [location_from_string(loc) for loc in ref["location"]]
refs.append(new_reference)
annotations["references"] = refs
return annotations
type="mRNA",
qualifiers=mrna_quals)
cds_joined_feature = SeqFeature(joined_loc,
type="CDS",
qualifiers=cds_quals)
new_feats.append(mrna_joined_feature)
new_feats.append(cds_joined_feature)
new_feats += utr_feats
if keep_rec:
rec.features = new_feats
rec.description = args.description
rec.annotations['organism'] = args.species
rec.annotations['taxonomy'] = lineage
rec.annotations['data_file_division'] = args.division
ref.location = [FeatureLocation(0, len(rec))]
rec.annotations['references'] = [ref]
rec.dbxrefs = [('Project:%s' % args.project)]
rec.annotations['keywords'] = [
'CON.'
] # CON is appropriate for scaffolds: https://www.ebi.ac.uk/training/online/course/nucleotide-sequence-data-resources-ebi/what-ena/how-sequence-assembled
SeqIO.write(rec, args.out, "embl")
def reformat_gbk(gbk_file,
study,
publication_title,
publication_authors,
publication_journal,
locus_tag_prefix,
taxon_id,
scaffold_prefix,
strain,
plasmid=False,
locus_count_start=1):
'''
- remove protein_id
- split scaffolds into contigs ==> name contigs contig_XXX
- generate agp file
:param gbk_file:
:param study:
:param publication:
:param locus_tag_prefix:
:param plasmid:
:return:
'''
source, taxonomy, organism = taxon_id2taxonomy(taxon_id)
print(source)
print()
print(taxonomy)
print()
new_records = []
from Bio import SeqIO
import copy
import copy
from Bio.SeqFeature import Reference
from Bio.SeqFeature import FeatureLocation
with open(gbk_file, 'r') as f:
records = [i for i in SeqIO.parse(f, 'genbank')]
#locus_count=1
contig_records = []
contig_count = 1
for new_record in records:
start = 0
end = len(new_record.seq)
print(dir(new_record))
for feature in new_record.features:
'''
if feature.type == 'assembly_gap':
print 'GAP-------'
print feature
contig = new_record[start:int(feature.location.start)]
# update start location
start = int(feature.location.end)
# rename contig record LOCUS
contig.id = "contig_%s" % contig_count
contig.name = "contig_%s" % contig_count
contig_records.append(contig)
contig_count += 1
'''
contig = new_record[start:end]
contig.id = "%s_%02d" % (scaffold_prefix, contig_count)
contig.name = "%s_%02d" % (scaffold_prefix, contig_count)
contig_records.append(contig)
contig_count += 1
for n, record in enumerate(contig_records):
ref = Reference()
ref.authors = publication_authors
ref.journal = publication_journal
ref.title = publication_title
'''
ref_seq = Refserence()
ref.authors = "Trestan Pillonel"
ref.journal = "RL Submitted (09-APRIL-2019) to the INSDC."
'''
#print record
#print dir(record)
#print "id", record.id
#print "name", record.name
#print record.annotations
#print record.description
#print record.dbxrefs
#record.id = ''
record.annotations['source'] = source
record.annotations['taxonomy'] = taxonomy
record.annotations['organism'] = organism
record.description = '%s %s scaffold_%s' % (organism, strain,
n + 1)
if record.features[0].type != 'source':
print('NOT SOURCE-------------------')
record.features = [copy.copy(record.features[0])
] + record.features
record.features[0].qualifiers = {}
record.features[0].type = 'source'
record.features[0].location = FeatureLocation(
0, len(record.seq))
else:
print('SOURCE!!!!!!!!!!!!!!!!')
record.features[0].qualifiers['db_xref'] = ["taxon:%s" % taxon_id]
record.features[0].qualifiers['mol_type'] = ["genomic DNA"]
record.features[0].qualifiers['organism'] = ["%s" % organism]
record.features[0].qualifiers['strain'] = ["%s" % strain]
if plasmid:
# /mol_type="genomic DNA"
# /organism="Klebsiella pneumoniae"
# /strain="KpGe"
#record.features[0].type = "source"
#record.features[0].qualifiers['organism'] = ["Klebsiella pneumoniae"]
#record.features[0].qualifiers['strain'] = ["KpGe"]
record.features[0].qualifiers['plasmid'] = ["p%s" % strain]
record.annotations['mol_type'] = ["genomic DNA"]
ref.location = [record.features[0].location]
#print 'location!', ref.location
record.annotations['references'] = [ref]
record.dbxrefs = ['BioProject:%s' % study]
for i, feature in enumerate(record.features):
if "protein_id" in feature.qualifiers:
del feature.qualifiers['protein_id']
if feature.type == 'gene':
'''
if not plasmid:
locus = "%s_%05d" % (locus_tag_prefix, locus_count)
else:
print 'rename locus!', locus_tag_prefix
locus = "%s_p%04d" % (locus_tag_prefix, locus_count)
'''
locus = "%s_%05d" % (locus_tag_prefix, locus_count_start)
locus_count_start += 1
feature.qualifiers['locus_tag'] = locus
record.features[i + 1].qualifiers['locus_tag'] = locus
new_records.append(record)
return new_records
