def rename(query_dir, input_dir):
namemap = {}
for i, filename in enumerate(sorted(os.listdir(input_dir)), 1):
file = SeqIO.parse(files.joinpath(input_dir, filename), "fasta")
records = []
for j, record in enumerate(file, 1):
newid = "Genome_{i}::Contig_{j}".format(**locals())
records.append(seq.new_record(newid, str(record.seq)))
newname = "Genome_{i}.fa".format(**locals())
SeqIO.write(records, files.joinpath(query_dir, newname), "fasta")
namemap[files.replace_ext(newname)] = files.replace_ext(filename)
return namemap
def reference_self_blastp(output_dir, freq):
ref_recs = [
seq.new_record(locus,
counter.most_common(1)[0][0].translate(table=11))
for locus, counter in freq.items()
]
ref_length = {rec.id: len(rec.seq) for rec in ref_recs}
ref_faa = os.path.join(output_dir, "ref_seq.faa")
seq.save_records(ref_recs, ref_faa)
ref_db = os.path.join(output_dir, "ref_db")
seq.compile_blastpdb(ref_faa, ref_db)
blastp_out_file = os.path.join(output_dir, "ref_db.blastp.out")
seq.query_blastpdb(ref_faa, ref_db, blastp_out_file, seq.BLAST_COLUMNS)
return blastp_out_file, ref_length
def make_ref_blastpdb(ref_db_file, database):
query = "select loci.locus_id, alleles.peptide_seq " \
"from loci inner join alleles " \
"on loci.ref_allele = alleles.allele_id;"
refs = db.from_sql(query, database=database)
ref_recs = [
seq.new_record(row["locus_id"], row["peptide_seq"], seqtype="protein")
for _, row in refs.iterrows()
]
ref_fasta = ref_db_file + ".fasta"
seq.save_records(ref_recs, ref_fasta)
ref_len = generate_allele_len(ref_recs)
seq.compile_blastpdb(ref_fasta, ref_db_file)
os.remove(ref_fasta)
return ref_len
def blast_for_new_alleles(candidates, alleles, ref_db, temp_dir, ref_len):
filename = "new_allele_candidates"
candidate_file = os.path.join(temp_dir, filename + ".fasta")
recs = [
seq.new_record(cand, alleles[cand][1], seqtype="protein")
for cand in candidates
]
seq.save_records(recs, candidate_file)
allele_len = generate_allele_len(recs)
blastp_out_file = os.path.join(temp_dir, "{}.blastp.out".format(filename))
seq.query_blastpdb(candidate_file, ref_db, blastp_out_file,
seq.BLAST_COLUMNS)
blastp_out = filter_duplicates(blastp_out_file,
allele_len,
ref_len,
identity=95)
blastp_out = blastp_out.drop_duplicates("qseqid")
new_allele_pairs = [(row["qseqid"], row["sseqid"])
for _, row in blastp_out.iterrows()]
return new_allele_pairs
def save_locusfiles(freq, locus_dir):
for locus, counter in freq.items():
records = [seq.new_record(operations.make_seqid(str(allele)), allele) for allele in counter.keys()]
seq.save_records(records, files.joinpath(locus_dir, locus + ".fa"))
def save_refseq(freq, refseq_file):
refseqs = {locus: counter.most_common(1)[0][0] for locus, counter in freq.items()}
records = [seq.new_record(str(locus), sequence) for locus, sequence in refseqs.items()]
SeqIO.write(records, refseq_file, "fasta")
return refseqs
def __write_new_format(self, source_file, sink_file):
records = []
for j, contig in enumerate(SeqIO.parse(source_file, "fasta"), 1):
seqid = self.newseqid(j)
records.append(seq.new_record(seqid, str(contig.seq)))
SeqIO.write(records, sink_file, "fasta")