extract_pos_from_sam.py 文件源码

def read_id2idx(reads_fn):

    if reads_fn[-1] == 'q':
        fmt = 'fastq'
    else:
        fmt = 'fasta'

    reads_idx={}
    reads_fh = open(reads_fn, "rU")
    num_read=0
    for record in SeqIO.parse(reads_fh, fmt):
        reads_idx[record.id] = num_read
        num_read += 1
    reads_fh.close()

    return reads_idx