subprocess.run and error codes

[srobb1]

https://github.com/prog4biol/evop2019/blob/master/EVOP_Python_2019.md/#use-error-code-to-control-pipeline

Use Error Code to Control Pipeline
If the error code is good (0) then we can proceed, if the error code is bad (!=0) stop.

#!/usr/bin/env python3
import subprocess
import sys

blastcmd = "blastx -query test.query -db ~/dbs/uniprot_sprot.fasta -outfmt 7 -out test.blastout.tab -evalue 1e-5"
countcmd = 'grep \'hits found\' test.blastout.tab  | perl -ne \'m/(\d+)/; $count=$1; print $count,"\n"\''

blastcmd_run = subprocess.run(blastcmd, shell=True , stdout = subprocess.PIPE, stderr=subprocess.PIPE)
if blastcmd_run.returncode == 0:
  # run count cmd if blast exit code is 0  
  countcmd_run = subprocess.run(countcmd,  shell=True , stdout = subprocess.PIPE, stderr=subprocess.PIPE)
else:
   sys.exit("BLAST had issues " + blastcmd_run.stderr.decode('utf-8'))


if countcmd_run.returncode == 0:
  if int(countcmd_run.stdout.decode('utf-8')) > 0:
    # parse results
    print("We will put parsing code here")
  else:
    sys.exit("no hits")
else:
  sys.exit("count had issues " + countcmd_run.stderr.decode('utf-8'))