Patch waiting problem with gunzip on line 91 of trenco_core

trenco2.py

@@ -3,8 +3,8 @@
 #
 # Wraper script for running all of trenco
 
-import sys, os, subprocess, re
-import glob, logging
+import os, json
+import logging
 import multiprocessing as mp
 import trenco_modules.trenco_args as targs
 import trenco_modules.trenco_core as tcore

trenco_modules/trenco_core.py

@@ -5,7 +5,7 @@ Trenco Modules for running scripts
 """
 
 import sys, os, glob, subprocess
-import logging
+import logging, time
 import shlex
 import pandas as pd
 import numpy as np
@@ -94,6 +94,8 @@ def process_tss(version, organism, biotypes, fname, logger):
                 #os.system(cmd) # the code needs to wait at this point
                 subprocess.check_call(cmd, shell=True)
 
+            time.sleep(30) # this is a temporary fix to make sure the gunzip works and has time
+
     if annotations.endswith('.gtf'):
         tail = '.gtf'
     else:

trenco_tools/get_encode_data.py

@@ -205,7 +205,11 @@ def get_df(df, assay_target, biosample_types, filter_age, output_type, file_type
         if assay_target == 'RNA-seq':
             target = assay
         elif assay == 'ChIP-seq':
-            target = r[1]['Experiment target'].split('-')[0]
+            try:
+                target = r[1]['Experiment target'].split('-')[0]
+            except:
+                continue
+                pass
         else:
             continue