1# read fasta file
2from Bio import SeqIO
3seq_dict = SeqIO.to_dict(SeqIO.parse(file_name, "fasta"))
4
5SeqIO.write(r_gene_seq_list, "r_gene_aa_v1_frozen.fa", "fasta")
6

 1# blast
 2output_file = f'r_gene_{genome_name}.xml'
 3blastp_cline = NcbiblastpCommandline(query="r_gene_merge.fa", db=work_db, evalue=0.001, outfmt=5, out=output_file)
 4print(blastp_cline)
 5stdout, stderr = blastp_cline()
 6
 7# parse blast
 8from Bio import SearchIO
 9blast_qresult = SearchIO.parse(xml_file, 'blast-xml')
10for qresult in blast_qresult:
11#        print(len(qresult))
12        for hit in qresult:
13            hit_list.append(hit.id)

1from Bio import SearchIO
2blast_qresult = SearchIO.parse(xml_file, 'hmmer3-tab') # or hmmer3-domtab
3
4