CODEWITHSUNDEEP
pythonbash
Perlnika
Perlnika

Reputation: 5056

Incorporate complex bash command into python

I need to call bash from python script and store result in the variable (the output is one number).

I need

output = subprocess.call('command', shell=True)

with command replaced by output from my bash one-liner which looks like this:

cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'

I know that simple commands work just fine:

    output = subprocess.check_output("echo 122;", shell=True)

My problem is that instead of 122 I need value from my bash one-liner. And it would be perfect if I didn't need to reformat it and could use it just as is.

Here are my attempts:

    output = subprocess.check_output("cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
    ", shell=True)

      File "script.py", line 9
        output = subprocess.check_output("cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
                                                                  ^
    SyntaxError: invalid syntax

Attempt two:

    output = subprocess.check_output("cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
", shell=True)

  File "script.py", line 9

    output = subprocess.check_output("cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
                                                                                                                                                                                                                    ^
SyntaxError: EOL while scanning string literal

Upvotes: 0

Views: 487

Answers (1)

Perlnika
Perlnika

Reputation: 5056

Thanks for help! Finally, this works:

command = "cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'";
process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
#Launch the shell command:
output = process.communicate()[0];

Upvotes: 1

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