find_good_orfs.py 文件源码

def write_genes(genes_align, outdir):
    records = []
    orfs = SeqIO.to_dict(SeqIO.parse(outdir+'ORFs.fasta', 'fasta'))
    for gene_cluster in genes_align:
        for orf in genes_align[gene_cluster][1]:
            if orfs[orf].seq is not None:
                records.append(SeqRecord.SeqRecord(seq=orfs[orf].seq, id='{0}_{1}'.format(gene_cluster, orf),
                                                   name='{0}_{1}_conf={2}_len={3}'.format(gene_cluster,
                                                                                          orf,
                                                                                          genes_align[gene_cluster][0],
                                                                                          len(orfs[orf]))))
    SeqIO.write(records, outdir+'results.fasta', 'fasta')