Importing tools into python

pyrpipe’s Runnable can be used to import any Unix command into python. The Runnable class implements the run() method which checks required dependencies, monitors execution, execute commands via pyrpipe_engine, and verify target files. We will first download the E. coli genome file to use as input to orfipy.

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
gunzip GCF_000005845.2_ASM584v2_genomic.fna.gz

Basic example

In this tutorial we will consider the tool orfipy, a tool for fast and flexible ORFs, and import it in python.

from pyrpipe.runnable import Runnable
infile='GCF_000005845.2_ASM584v2_genomic.fna'
#create a Runnable object
orfipy=Runnable(command='orfipy')
#specify orfipy options; these can be specified into orfipy.yaml too
param={'--outdir':'orfipy_out','--procs':'3','--dna':'orfs.fa'}
orfipy.run(infile,**param)

Save the above script in example.py and execute it using python example.py –dry-run. pyrpipe should generate the orfipy command and display on screen during dry-run. Running it without –dry-run flag will generate the orfipy_out/orfs.fa file.

Requirements and targets

One can specify required dependencies and expected target files in the run() method Replacing the call to run() with the following will verify the required files and the target files. If command is interrupted, pyrpipe will scan for Locked taget files and resume from where the pipeline was interrupted.

orfipy.run(infile,requires=infile,target='orfipy_out/orfs.fa',**param)