update for quality update file location for conda

Author: maxibor

lib/adrsmlib.py

@@ -2,6 +2,8 @@
 
 import sys
 import requests
+import os
+import subprocess
 from numpy import random as npr
 import multiprocessing
 import pickle
@@ -168,6 +170,30 @@ def markov_multi_rev(process, nreads):
     return(r)
 
 
+def get_fwd_qual():
+    try:
+        pickle.load(open("fwd_qual.p", 'rb'))
+    except FileNotFoundError:
+        cmd = "which adrsm"
+        res = subprocess.check_output(cmd, shell=True)
+        res = res.decode('utf-8').rstrip()
+        path = "/".join(res.split("/")[:-2])+"/data/quality/fwd_qual.p"
+        ret = pickle.load(open(path, 'rb'))
+    return(ret)
+
+
+def get_rev_qual():
+    try:
+        pickle.load(open("fwd_qual.p", 'rb'))
+    except FileNotFoundError:
+        cmd = "which adrsm"
+        res = subprocess.check_output(cmd, shell=True)
+        res = res.decode('utf-8').rstrip()
+        path = "/".join(res.split("/")[:-2])+"/data/quality/rev_qual.p"
+        ret = pickle.load(open(path, 'rb'))
+    return(ret)
+
+
 def run_read_simulation_multi(INFILE, COV, READLEN, INSERLEN, NBINOM, A1, A2, MINLENGTH, MUTATE, MUTRATE, AGE, ERR,  DAMAGE, GEOM_P, THEMIN, THEMAX, fastq_dict, PROCESS):
     print("===================\n===================")
     print("Genome: ", INFILE)
@@ -203,8 +229,8 @@ def run_read_simulation_multi(INFILE, COV, READLEN, INSERLEN, NBINOM, A1, A2, MI
     print("-------------------")
 
     MARKOV_ORDER = 7
-    QUALIT_FWD = pickle.load(open('data/quality/fwd_qual.p', 'rb'))
-    QUALIT_REV = pickle.load(open('data/quality/rev_qual.p', 'rb'))
+    QUALIT_FWD = get_fwd_qual()
+    QUALIT_REV = get_rev_qual()
     MARKOV_SEED_FWD = mk.generate_kmer(
         qualities=QUALIT_FWD, order=MARKOV_ORDER, readsize=READLEN)
     MARKOV_SEED_REV = mk.generate_kmer(