Gscripts

The code provided herein is without any warranty.

It is mostly development code, bugs and inefficiencies are likely, please report any problems to the gscripts issues page.

How to install gscripts

cd path/to/gscripts; easy_install . 

(NOT pip)

How to import qtools

from gscripts.qtools import Submitter

For example, to submit a single line of code to a compute job, you can do:

from gscripts.qtools import Submitter

exon_seqs = '/projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2.fasta'
mirna_seqs = '/projects/ps-yeolab/genomes/mirbase/release_21/human_mature_17bp.fa'
rnahybrid_results = '/projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2_RNAhybrid_mirbase_human_mature_17bp.txt'
command = 'RNAhybrid -c -s 3utr_human -q {} -t {} > {}'.format(mirna_seqs, exon_seqs, rnahybrid_results)
sub = Submitter([command], 'RNAhybrid', walltime='120:00:00', write_and_submit=True, nodes=1, ppn=1)

Which will write a file called RNAhybrid.sh which has these contents:

#!/bin/bash
#PBS -N RNAhybrid
#PBS -o RNAhybrid.sh.out
#PBS -e RNAhybrid.sh.err
#PBS -V
#PBS -l walltime=120:00:00
#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
RNAhybrid -c -s 3utr_human -q /projects/ps-yeolab/genomes/mirbase/release_21/human_mature_17bp.fa -t /projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2.fasta > /projects/ps-yeolab/obotvinnik/miso_helpers/hg19/se_exon2_RNAhybrid_mirbase_human_mature_17bp.txt

How to import Python version of which

from gscripts import which