make_target_tf.py and param4net.py: add an option EXISTING_TARGET_TF_PAIRS in parameter_for_net.txt to specify locations of existing Target-TF pairs.

1 files changed, 17 insertions, 26 deletions

diff --git a/Code/make_target_tf.py b/Code/make_target_tf.py
index 06bc769..cb1775b 100644
--- a/Code/make_target_tf.py
+++ b/Code/make_target_tf.py
@@ -240,32 +240,22 @@ def target_tf(bind_dict, bind_info_dict, input_dict, glb_param_dict):
     # d has the following format {target:{tf1:[c1,c2], tf2:[c2,c3]}, ...  }

 

     # augment d with information from ../Data/information/target_tf_agris.txt and ../Data/information/target_tf.txt.20170629_143000

-    if os.path.exists('../Data/information/target_tf_agris.txt'):

-        f = open('../Data/information/target_tf_agris.txt')

-        lines = f.readlines()

-        f.close()

-        for line in lines:

-            line = line.strip()

-            lst = line.split('\t')

-            if len(lst) == 3:

-                target0 = lst[0]

-                tf0     = lst[1]

-                cond_lst0  = lst[2].split()

-                augment_dict(d, target0, tf0, cond_lst0)

-                

-    if os.path.exists('../Data/information/target_tf.txt.20170629_143000'):

-        f = open('../Data/information/target_tf.txt.20170629_143000')

-        lines = f.readlines()

-        f.close()

-        for line in lines:

-            line = line.strip()

-            lst = line.split('\t')

-            if len(lst) == 3:

-                target0 = lst[0]

-                tf0     = lst[1]

-                cond_lst0  = lst[2].split()

-                augment_dict(d, target0, tf0, cond_lst0)

-    

+    if glb_param_dict['EXISTING_TARGET_TF_PAIRS'] != None:

+        target_tf_file_lst = glb_param_dict['EXISTING_TARGET_TF_PAIRS'].split()

+        for existing_target_tf_file in target_tf_file_lst:

+            if os.path.exists(existing_target_tf_file):

+                f = open(existing_target_tf_file)

+                lines = f.readlines()

+                f.close()

+                for line in lines:

+                    line = line.strip()

+                    lst = line.split('\t')

+                    if len(lst) == 3:

+                        target0 = lst[0]

+                        tf0     = lst[1]

+                        cond_lst0  = lst[2].split()

+                        augment_dict(d, target0, tf0, cond_lst0)

+                    

     for target in sorted(d.keys()):

         tf_d = d[target]

         if len(tf_d) > 0:

@@ -279,6 +269,7 @@ def target_tf(bind_dict, bind_info_dict, input_dict, glb_param_dict):
 ########## main ##################################################

 param_file = sys.argv[1] # a single prameter file parameter_for_net.txt

 glb_param_dict = make_global_param_dict(param_file)

+

 #print('Read binding data ...')

 bind_dict = read_matrix_data(glb_param_dict['BINDING_MATRIX'])

 bind_info_dict = read_info_data(glb_param_dict['BINDING_INFO'])