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calling BWA mem from within python

Dear all,

I would like to call BWA mem from within a python script. This works, but I cannot specify an output filename. The output is printed to stdout, but off course this is not what I want. From within BWA I should use '>' but this is not working from within python. This is the call function that I'm using: 

aln_value=call([script_dir+"/software/bwa","mem", "-t 4", "-M", script_dir+"/ref/hg19.navin", args.fastq_file ],stderr=ERR_LOG,stdout=OUT_LOG)

Is there a simple alternative that allows me to specify the outputfile from within the python script?

Thanks , Lien

bwa mem python
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updated by Charles-Alexandre Roy • Charles-Alexandre Roy • written by lien lien

You can build the command as a string in python however you want, then run the command using os.system:

import os
cmd = "bwa mem -t 4 -M " + script_dir + "/ref/hg19.navin " + fastq_file + " > output"
os.system(cmd)
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written by Damian Kao Damian Kao

Thanks, this worked for me (Python 3.7). It seems that BWA doesn't work properly with os.subprocess(), but instead os.system() works perfectly. The bug about os.subprocess() should be something with output handling, I'm not sure.

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written by Benedek Dankó • Benedek Dankó

1 answer

Take a look at subprocess

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written by Picasa Picasa

This would be the ideal option as it would let you rebuild shell style pipelines in python. Something like bwa mem .... | samtools view ...

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written by pld pld

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