qtools

What is qtools?

qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python

• Free software: BSD license

Installation

To install this code, clone this github repository and use pip to install

git clone git@github.com:YeoLab/qtools
cd qtools
pip install .  # The "." means "install *this*, the folder where I am now"

Features

Simple example

Here's an example of a single job where I want to use hmmscan to find domains in protein sequences, specifying the walltime and number of processors.

import qtools

command = 'bedtools intersect exons.bed placental_conserved_elements.bed'
sub = qtools.Submitter(command, 'intersect')

And this will create a submitter script with the default options:

• walltime="00:30:00"
• nodes=1
• ppn=1 (processors per node - increase this one first, instead of the numbers of nodes. Max is 16)
• group="yeo-group"
• queue="home-scrm" (could also be home-yeo

This writes a file called intersect.sh which looks like this:

#!/bin/bash
#PBS -N intersect
#PBS -o intersect.out
#PBS -e intersect.err
#PBS -V
#PBS -l walltime=00:30:00
#PBS -l nodes=1:ppn=1
#PBS -A yeo-group
#PBS -q home

# Go to the directory from which the script was called
cd $PBS_O_WORKDIR
bedtools intersect exons.bed placental_conserved_elements.bed

The output is:

job ID: 3610818

Array job example

If you have a bunch of independent jobs you want to run, then you can submit them with one command using array=True. Here's an example of calculating average conservation of both constitutive and alternative exons.

import os
import glob

import qtools

folder = '/projects/ps-yeolab/obotvinnik/singlecell_pnms'

alt_exons_bedfile = '{}/exon2.bed'.format(folder)
constitutive_bedfile = '{}/constitutive_exons.bed'.format(folder)

bedfiles = alt_exons_bedfile, constitutive_bedfile

commands = []

bw = '/projects/ps-yeolab/genomes/hg19/hg19_phastcons_placental_mammal.bw'

for bedfile in bedfiles:
    basename = os.path.basename(bedfile)

    prefix = basename.split('.bed')[0]

    prefix += '_phastcons_placental_mammal'
    bedout = '{}/{}'.format(folder, prefix + '.bed')
    outtab = '{}/{}'.format(folder, prefix + '.txt')
    command = 'bigWigAverageOverBed {} {} {} -bedOut={}'.format(bw, bedfile, outtab, bedout)
    print command
    commands.append(command)

jobname = 'exonbody_conservation'
qtools.Submitter(commands, jobname, array=True, walltime='2:00:00')

Output:

running 2 tasks as an array-job.
job ID: 3614584

This creates the file exonbody_conservation.sh which looks like this:

#!/bin/bash
#PBS -N exonbody_conservation
#PBS -o /projects/ps-yeolab/obotvinnik/singlecell_pnms/exonbody_conservation.out
#PBS -e /projects/ps-yeolab/obotvinnik/singlecell_pnms/exonbody_conservation.err
#PBS -V
#PBS -l walltime=2:00:00
#PBS -l nodes=1:ppn=1
#PBS -A yeo-group
#PBS -q home
#PBS -t 1-2

# Go to the directory from which the script was called
cd $PBS_O_WORKDIR
cmd[1]="bigWigAverageOverBed /projects/ps-yeolab/genomes/hg19/hg19_phastcons_placental_mammal.bw /projects/ps-yeolab/obotvinnik/singlecell_pnms/exon2.bed /projects/ps-yeolab/obotvinnik/singlecell_pnms/exon2_phastcons_placental_mammal.txt -bedOut=/projects/ps-yeolab/obotvinnik/singlecell_pnms/exon2_phastcons_placental_mammal.bed"
cmd[2]="bigWigAverageOverBed /projects/ps-yeolab/genomes/hg19/hg19_phastcons_placental_mammal.bw /projects/ps-yeolab/obotvinnik/singlecell_pnms/constitutive_exons.bed /projects/ps-yeolab/obotvinnik/singlecell_pnms/constitutive_exons_phastcons_placental_mammal.txt -bedOut=/projects/ps-yeolab/obotvinnik/singlecell_pnms/constitutive_exons_phastcons_placental_mammal.bed"
eval ${cmd[$PBS_ARRAYID]}

Direct stdout/stderr to a specific location, and specify queue or number of processors

If you want your sh/stdout/stderr to be sent to a specific location, instead of to the folder you're currently in by default, then specify them with sh, out, and err. You can also specify the queue (home-yeo vs home-scrm) with queue="home-scrm". The default is home-yeo.

import qtools

jobname = 'run_outrigger_py'
sh = jobname + '.sh'
out = sh + '.out'
err = sh + '.err'

command = 'python /projects/ps-yeolab/obotvinnik/singlecell_pnms/outrigger/outrigger.py'

n_processors = 16
sub = qtools.Submitter([command], 'run_outrigger_py', queue='home-yeo',
                out=out, err=err, sh=sh, walltime='100:00:00', nodes=1,
                ppn=n_processors)

Output:

job ID: 3884631