init_schema_4_bbaca.py 文件源码

def get_Short(genesList):
    for gene in genesList:
        # gene = gene.rstrip('\n')
        pathtoDir = os.path.join(os.path.dirname(gene), "short")
        if not os.path.exists(pathtoDir):
            os.makedirs(pathtoDir)
        shortgene = os.path.join(os.path.dirname(gene), "short", os.path.basename(gene))
        shortgene = shortgene.replace(".fasta", "_short.fasta")

        #gene_fp2 = HTSeq.FastaReader(gene)
        for allele in SeqIO.parse(gene, "fasta", generic_dna):
            fG = open(shortgene, 'w')
            fG.write('>' + str(allele.id) + '\n' + str(allele.seq.upper()) + '\n')
            fG.close()
            break

    return True