Genome_Annotation.py 文件源码

def filter_evm_gff(evm_path):
    os.chdir(evm_path)
    ds = [f for f in os.listdir(evm_path) if os.path.isdir(f)]
    out_h = open('evm.evidence.txt','w')
    for d in ds:
        fPath = d + '/evm.out'
        size = os.path.getsize(fPath)
        if size > 0:
            blocks = open(fPath).read().strip().split('#')[1:]
            for block in blocks:
                coords = []
                evidence = []
                for line in block.strip().split('\n')[1:]:
                    if line.strip() != '' and line[0] != '!':
                        meta = line.strip().split('\t')
                        coords.append(int(meta[0]))
                        coords.append(int(meta[1]))
                        coords.sort()
                        evidence.extend([tuple(x[1:-1].split(';')) for x in meta[-1].split(',')])

                evidence = set(evidence)
                sources = set([x[1] for x in evidence])

                out_h.write(d + '\t' + str(coords[0]) + '\t' + str(coords[-1]) + '\t' + ','.join([x[0] for x in evidence]) + '\t' + ','.join(sources) + '\n')
    out_h.close()