ltr variables via environment variables

mgescan/.mgescan.cfg

@@ -0,0 +1,31 @@
+# HMMER Version to use
+#MGESCAN_HMMER_VERSION=3
+
+###############
+# LTR variables
+###############
+
+#min_dist: minimum distance(bp) between LTRs.
+#MGESCAN_MIN_DISTANCE=2000
+
+#max_dist: maximum distance(bp) between LTRS
+#MGESCAN_MAX_DISTANCE=20000
+
+#min_len_ltr: minimum length(bp) of LTR.
+#MGESCAN_MIN_LENGTH_LTR=130
+
+#max_len_ltr: maximum length(bp) of LTR.
+#MGESCAN_MAX_LENGTH_LTR=2000
+
+#ltr_sim_condition: minimum similarity(%) for LTRs in an element.
+#MGESCAN_LTR_SIMILARITY=70
+
+#cluster_sim_condition: minimum similarity(%) for LTRs in a cluster
+#MGESCAN_LTR_SIMILARITY_CLUSTER=70
+
+#len_condition: minimum length(bp) for LTRs aligned in local alignment.
+#MGESCAN_MIN_LENGTH=70
+
+#MGESCAN_REPEATMASKER=No
+
+#MGESCAN_SCAFFOLD_DIR=

mgescan/cmd.py

@@ -40,6 +40,7 @@ def __init__(self, args):
         self.args = args
         self.set_inputs()
         self.set_defaults()
+        self.get_env()
         self.set_env()
 
     def set_inputs(self):
@@ -81,6 +82,18 @@ def set_defaults(self):
         self.sw_rm = "No" # or Yes
         self.scaffold = "" # or directory
 
+    def get_env(self):
+        self.hmmerv = os.environ.get("MGESCAN_HMMER_VERSION") or self.hmmerv
+        self.min_dist = os.environ.get("MGESCAN_MIN_DISTANCE") or self.min_dist
+        self.max_dist = os.environ.get("MGESCAN_MAX_DISTANCE") or self.max_dist
+        self.min_len_ltr = os.environ.get("MGESCAN_MIN_LENGTH_LTR") or self.min_len_ltr
+        self.max_len_ltr = os.environ.get("MGESCAN_MAX_LENGTH_LTR") or self.max_len_ltr
+        self.ltr_sim_condition = os.environ.get("MGESCAN_LTR_SIMILARITY") or self.ltr_sim_condition
+        self.cluster_sim_condition = os.environ.get("MGESCAN_LTR_SIMILARITY_CLUSTER") or self.cluster_sim_condition
+        self.len_condition = os.environ.get("MGESCAN_MIN_LENGTH") or self.len_condition
+        self.sw_rm = os.environ.get("MGESCAN_REPEATMASKER") or self.sw_rm
+        self.scaffold = os.environ.get("MGESCAN_SCAFFOLD_DIR") or self.scaffold
+
     def set_env(self):
         self.base_path = os.environ.get('MGESCAN_SRC') + "/mgescan"
         if not self.base_path: