Update Trenco code to weight expressed genes

trenco2.py

 #!/usr/bin/env python3
-
-#
-# Wraper script for running all of trenco
-
-import os, json
+# --------------------------------------------------------------------------- #
+# Wraper script for running all of trenco. The main scripts are found in      #
+# trenco_core module and are imported.                                        #
+#                                                                             #
+# Inputs required:                                                            #
+# DESIGN     tab separated file containing link information of samples        #
+#               to names                                                      #
+# ALIGNMENT  bam files form ChIP-seq experiments for enhancers                #
+# BED        file of TAD regions to use                                       #
+# EXPRESSION tsv file containing transcript expression                        #
+# PEAKS bed  files with called enhancer peaks                                 #
+# ANNOTAIONS gtf file vM4 recommended with gene annotations                   #
+#                                                                             #
+# Major Outputs:                                                              #
+# Three folders:                                                              #
+#   - Results - contains graph results of the networks                        #
+#   - Log     - contains the logs of the scripts                              #
+#   - Process - contains intermediate files and plots                         #
+# EDGE csv formatted information containing graph link information between    #
+#       in an array                                                           #
+# NODE csv formatted information containining expression data for each gene   #
+#       node                                                                  #
+# --------------------------------------------------------------------------- #
+
+import os
+import json
 import logging
 import multiprocessing as mp
 import trenco_modules.trenco_args as targs
@@ -102,6 +123,16 @@ def initial_setup(version,
 
     return (bedgene, bedenh, txn_log2TPM, enh_log2TPM, mtcs[0], mtcs[1])
 
+def _DEBUG():
+    bedgene     = "process/gene.bed" 
+    bedenh      = "process/enh.bed" 
+    txn_log2TPM = "process/transcript_expression_log2TPM_matrix.txt" 
+    enh_log2TPM = "process/enhancer_H3K27ac_log2TPM_signal_matrix.txt" 
+    mtx1        = "process/TFxgencode.vM4.annotation_capped_sites_"\
+                        "1000u200d_promoter.bed_score_matrix.txt" 
+    mtx2        = "process/TFxenh.bed_score_matrix.txt"
+    return (bedgene, bedenh, txn_log2TPM, enh_log2TPM, mtx1, mtx2)
+
 def full_build(samples,
                gene,
                enh,
@@ -132,7 +163,10 @@ def full_build(samples,
 if __name__ == '__main__':
     parser = ArgumentParser(
         description = "TAD aware Regulatory Network Construction (TReNCo)",
-        usage="trenco --design [DESIGN FILE (txt)] --alignment [ALIGNMENT FILES (tsv)] --expression [EXPRESSION FILES (bam)] --peaks [PEAK FILES (bed)] -g [GENOME VERSION] [OPTIONS]")
+        usage="trenco --design [DESIGN FILE (txt)] \
+                --alignment [ALIGNMENT FILES (tsv)] \
+                --expression [EXPRESSION FILES (bam)] \
+                --peaks [PEAK FILES (bed)] -g [GENOME VERSION] [OPTIONS]")
 
     targs.full_trenco_args(parser)
     targs.enh_bound_args(parser, False)
@@ -141,7 +175,11 @@ if __name__ == '__main__':
     
     args = parser.parse_args()
 
-    files = [args.peaks, args.alignment, args.expression, args.tadBED, args.design]
+    files = [args.peaks, 
+             args.alignment, 
+             args.expression, 
+             args.tadBED, 
+             args.design]
     for fi in files:
         if not isinstance(fi, list):
             fi = [fi]
@@ -154,7 +192,8 @@ if __name__ == '__main__':
     peaks, alignments, expressions, tads, design = files
     prange = [int(x) for x in args.promoter_range.split("-")]
 
-    design_key, design_key_inv = {}, {}
+    design_key     = {}
+    design_key_inv = {}
     with open(design, 'r') as ifi:
         for line in ifi:
             line = line.split()
@@ -174,21 +213,35 @@ if __name__ == '__main__':
         args.gvers = _ORAGNISM_GENOME[args.organism]
 
     if not debug:
-        geneBED, enhBED, txn_log2TPM, enh_log2TPM, tf_gene_mx, tf_enh_mx = initial_setup(args.annotations,
-                    args.organism,
-                    args.biotypes,
-                    args.annotfname,
-                    args.region, 
-                    args.distance, 
-                    peaks, 
-                    prange,
-                    args.expression,
-                    args.alignment,
-                    args.target,
-                    args.gvers,
-                    args.meme_db,
-                    memedb,
-                    logger)
+        geneBED, \
+          enhBED, \
+          txn_log2TPM, \
+          enh_log2TPM, \
+          tf_gene_mx, \
+          tf_enh_mx \
+            = initial_setup(args.annotations,
+                            args.organism,
+                            args.biotypes,
+                            args.annotfname,
+                            args.region, 
+                            args.distance, 
+                            peaks, 
+                            prange,
+                            args.expression,
+                            args.alignment,
+                            args.target,
+                            args.gvers,
+                            args.meme_db,
+                            memedb,
+                            logger)
+    else:
+        geneBED, \
+          enhBED, \
+          txn_log2TPM, \
+          enh_log2TPM, \
+          tf_gene_mx, \
+          tf_enh_mx \
+            = _DEBUG()    
     
     full_build(design_key,
                txn_log2TPM,