Question

在使用pysam模块时，我尝试将stdout重定向到文件，如下所示：

bam=sys.argv[1]
samfile = pysam.AlignmentFile(bam, "rb")
for alignment in samfile:
    reverse=isReverse(alignment.flag)
    if (reverse):
        outfile = pysam.AlignmentFile("-", "w", template=samfile)
        with open('reverse.sam', 'w') as f:
            with (f):
                for s in samfile:
                    print('HEY')
                    outfile.write(s)

当“print（'HEY'）”写入reverse.sam时，“outfile.write（s）”不是。我应该怎么做呢？谢谢标记

Answer 1

不应该

for alignment in samfile.fetch()

？什么

type (alignment)

得到？你有什么打算用额外的

with (f)

上下文？ :)从你发布的内容来看，外部环境已经没有意义了。

Answer 2

你走了。

bam_file = sys.argv[1]  # or '-' (if reading from stdin) or 'path/to/your/input.bam'
sam_file = 'path/to/your/output.sam'  # or '-' (if writing to stdout) or 'path/to/your/output.bam' (for bam file)

infile = pysam.AlignmentFile(bam_file, "rb")
outfile = pysam.AlignmentFile(sam_file, "w", template=infile)  # or "wb" if writing to bam file

i = 0

for alignment in infile:
    if alignment.is_reverse:
        outfile.write(alignment)
        i += 1

outfile.close()
infile.close()
print("Wrote {} alignments.".format(i))

将stdout重定向到文件

2 个答案: