Bowtie2 and subprocess issue

Question

[robjohn70000]

Hi,

I tried running bowtie2 in python using subprocess without any success.

Codes:

REFGENOME='/path-to-genome/genome.fasta'

P1='/path-to-fastq/P1.fastq.bz2'
P2='/path-to-fastq/P2.fastq.bz2'

cmd=['bowtie2','--quiet','-p','10','--dovetail','--no-head','--no-sq','-x',REFGENOME,'-1',P1,'-2',P2,'-S', 'out.sam']

subprocess.Popen(cmd, shell=True)

Error:

No index, query, or output file specified!

Does anyone know how to set up subprocess properly to get the code working?

Answer 1

[Dave Carlson]

I typically use subprocess.run for this sort of thing. The following works (tested with python 3.7):

#!/usr/bin/env python

import subprocess

REFGENOME='path/to/indexed/genome.fasta'

P1='/path/to/r1.fq.gz'
P2='path/to/r2.fq.gz'

cmd=['bowtie2','--quiet','-p','10','--dovetail','--no-head','--no-sq','-x',REFGENOME,'-1',P1,'-2',P2,'-S', 'out.sam']

subprocess.run(cmd)

[robjohn70000]

@Dave Carlson your solution worked for me. Many thanks!