dbprep.py 文件源码

def indexFile(options):
    filename=options.output
    if not options.ensembl is None:
        sys.stdout.write('Compressing output file... ') 
        sys.stdout.flush()
        pysam.tabix_compress(filename,filename+'.gz',force=True)
        sys.stdout.write('OK\n')    
        sys.stdout.write('Indexing output file... ') 
        sys.stdout.flush()
        pysam.tabix_index(filename+'.gz', seq_col=2, start_col=4, end_col=5, meta_char='#',force=True)
        sys.stdout.write('OK\n')
    else:
        print 'Compressing file...'
        pysam.tabix_compress(filename,filename+'.gz',force=True)
        print 'Indexing file...'
        pysam.tabix_index(filename+'.gz', seq_col=1, start_col=2, end_col=2, meta_char='#',force=True)

# Sort records in file