reports.py 文件源码

def mga_summary(orf_fp, contigs_fp, sample_id):
    """Summarizes results from MetaGene Annotator."""
    genes = []
    gene_no = 0
    contigs = SeqIO.parse(contigs_fp, 'fasta')
    contig_seqs = {r.description: r.seq for r in contigs}
    annotations = MetaGeneAnnotation.parse(open(orf_fp))
    for anno in annotations:
        contig_seq = contig_seqs[anno.id]
        # Gather putative genes and create SeqRecords for them
        for pgene in anno.genes:
            gene_seq = contig_seq[pgene.start:pgene.end]
            if pgene.strand == '-':
                gene_seq = gene_seq.reverse_complement()
            gene = SeqRecord(
                gene_seq,
                id=anno.id,
                description="{}:{}".format(sample_id, gene_no))
            genes.append(gene)
            gene_no += 1
    return genes