Refactor to use helper function

script/make_nopped_op_variants.py

@@ -7,6 +7,8 @@
 
 from keyname import keyname as kn
 
+from pyhelpers import genome_local_autoload
+
 try:
     __, applyto, basedon = sys.argv
 except:
@@ -17,29 +19,8 @@
 assert 'ext' in kn.unpack( applyto )
 assert 'ext' in kn.unpack( basedon )
 
-def multiloader(target):
-    if kn.unpack( target )['ext'] == '.json':
-        with open( target, 'r') as f:
-            return json.load( f )
-
-    elif kn.unpack( target )['ext'] == '.json.gz':
-        try:
-            with gzip.open( target, 'rb') as f:
-                return json.loads( f.read().decode('ascii') )
-        except Exception:
-            pass
-
-        try:
-            with gzip.open( target, 'rb') as f:
-                return json.loads( f.read().decode('utf-8') )
-        except Exception:
-            pass
-
-    raise ValueError
-
-
-applytodata = multiloader( applyto )
-basedondata = multiloader( basedon )
+applytodata = genome_local_autoload( applyto )
+basedondata = genome_local_autoload( basedon )
 
 assert (
     len( applytodata['value0']['program'] )

slurm/genomes/nopoutjob.slurm.sh.jinja

@@ -277,9 +277,7 @@ echo "----------------------------------------------------------"
 timeout 30s "${REPRO_WORK_DIRECTORY}/dishtiny/script/host_squeue.sh" -j "${SLURM_JOB_ID}" --format \"time: %M, time left: %L\" --noheader || echo "time log failed" &
 wait # ignores exit code of time log step
 
-# adapted from https://superuser.com/a/689340
-# and https://stackoverflow.com/a/31687663
-wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 10 -qO- https://raw.githubusercontent.com/mmore500/dishtiny/{{ repo_sha }}/script/make_nopped_op_variants.py | python3 - "${WILDTYPE_GENOME}" "${PHENOTYPE_EQUIVALENT_GENOME}"
+"${REPRO_WORK_DIRECTORY}/dishtiny/script/make_nopped_op_variants.py" | python3 - "${WILDTYPE_GENOME}" "${PHENOTYPE_EQUIVALENT_GENOME}"
 
 ################################################################################
 echo