<p>It's a bit hard to say with certainty, though I would suspect that offloading the BAM decompression by using a pipe will be very slightly faster. Note that decompressing and parsing the BAM file will not be the bottleneck in your processing, rather the python script itself will be.</p>

CC BY-SA 4.0
2019-12-11T21:51:34.613Z
2019-12-11T21:51:34.613Z
Devon Ryan
<p>Is it faster to use the PySam package to run a python script on a bam</p>

<pre><code>for read in samfile.fetch('chr1', 100, 120):
 print read
</code></pre>

<p>compared to using a pipe and reading line by line from stdin in a python script. </p>

<p><code>samtools view example.bam | python script.py.
</code></p>

<pre><code>for line in tqdm(sys.stdin, total=number_of_lines)
</code></pre>

<python><sam><samtools><pysam>
pysam or piping samtools view to a python script
# pysam or piping samtools view to a python script

(Asked by: username_0 on 2019-12-11)

Is it faster to use the PySam package to run a python script on a bam
for read in samfile.fetch('chr1', 100, 120):
 print read

compared to using a pipe and reading line by line from stdin in a python script. 
samtools view example.bam | python script.py.

for line in tqdm(sys.stdin, total=number_of_lines)

**Tags:** python, sam, samtools, pysam

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## 1 answers

### Answer by username_1 on 2019-12-11. Score: 5

It's a bit hard to say with certainty, though I would suspect that offloading the BAM decompression by using a pipe will be very slightly faster. Note that decompressing and parsing the BAM file will not be the bottleneck in your processing, rather the python script itself will be.


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