How to call BBMap, SAMTools and GATK from Python or Ruby?

Question

[vassialk]

How to call BBMap, SAMTools and GATK from Python or Ruby? Need some example scripts, please.

[h.mon]

Google would help you a lot. StackOverflow as well, there are tons of similar questions there. E.g. for Python here and here, and for Ruby here and here.

Answer 1

[Devon Ryan]

In python use the subprocess library. No clue about Ruby, though it has an equivalent of making system calls.

[vassialk]

thank you, are there any actual sample scripts available somewhere?

Answer 2

[Tky]

You can search the GitHub with keyword "GATK", on the left panel 

Select "Code" and in Language section, check "Python".

Here is one actual script from this link ,  there are 2000+ such scripts, you should be able to find some useful ones for your project. And you can do same for Ruby as well. 

from package import *

class gatk(Package):
    dependencies = ['jre_oracle']
    def fetch(self):
        f = self.fillVars('%(srcpath)s/GenomeAnalysisTK-3.3-0.tar.bz2')
        if not os.path.isfile(f):
            error('Please supply source file: %s' %f)
        return f
    
    workdir="gatk-3.3-0"
    create_workdir=True

    build="""
        mkdir -p %(prefix)s/opt/gatk
        cp -R * %(prefix)s/opt/gatk
        cd %(prefix)s/opt/gatk
        """

    install="""
        cd %(prefix)s/opt/gatk
        echo "#!/bin/bash" > gatk
        echo "java -jar %(prefix)s/opt/gatk/GenomeAnalysisTK.jar \$@" >> gatk
        chmod +x gatk
        cp ./gatk %(prefix)s/bin/
    """ 

[vassialk]

Thank you --------------------------

Answer 3

[kojix2]

In Ruby, you can call Unix commands using system, backquotes, open3, spawn, etc. You can also use the Rake and sh. In many cases, system is sufficient, but do you want neat terminal outputs and useful tools? If so, tty-command is a good option.

https://github.com/piotrmurach/tty-command.

cmd.run("samtools version" )

[Trivas]

With python you can do os.system with a string that you create that matches what you would type into the command line

Answer 4

[Roman Luštrik]

You can run it using package plumbum.

from plumbum import local

samtools = local['samtools']  # or relative/absolute path to samtools
print(samtools['--help']())

Output:

Program: samtools (Tools for alignments in the SAM format)
Version: 1.8 (using htslib 1.8)
Usage:   samtools <command> [options]
Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment