Mercurial > repos > bimib > cobraxy

changeset 289:3f5cfcf4d9eb draft

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Uploaded
author francesco_lapi
date Wed, 14 May 2025 10:08:09 +0000
parents d1d732d1705c
children 71ec0b6ddde9
files COBRAxy/marea.py
diffstat 1 files changed, 2 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/marea.py	Wed May 14 10:04:23 2025 +0000
+++ b/COBRAxy/marea.py	Wed May 14 10:08:09 2025 +0000
@@ -371,10 +371,8 @@
     Returns:
         Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
     """
-    print("getArrowHeadElementId: ", reactionId)
     if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
     elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown:
-        print(f"getArrowHeadElementId: {reactionId} this was not unknown.")
         return reactionId[:-3:-1] + reactionId[:-2], "" # ^^^ Invert _F to F_
 
     return f"F_{reactionId}", f"B_{reactionId}"
@@ -384,7 +382,6 @@
     Encodes possible arrow colors based on their meaning in the enrichment process.
     """
     Invalid       = "#BEBEBE" # gray, fold-change under treshold
-    Transparent   = "#ffffff00" # transparent, not significant p-value
     UpRegulated   = "#ecac68" # orange, up-regulated reaction
     DownRegulated = "#6495ed" # lightblue, down-regulated reaction
 
@@ -427,10 +424,8 @@
         self.dash = isDashed
     
     def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
-        #if 
-        getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).unwrap()
-        #.isErr:
-        #    ERRORS.append(reactionId)
+        if getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).isErr:
+            ERRORS.append(reactionId)
 
     def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
         # If We're dealing with RAS data or in general don't care about the direction of the reaction we only style the arrow body
@@ -439,7 +434,6 @@
         
         # Now we style the arrow head(s):
         idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
-        print("styleReactionElements: ", idOpt1, idOpt2)
         self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
         if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
     
@@ -502,12 +496,10 @@
 
         if isinstance(foldChange, str): foldChange = float(foldChange)
         if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
-            print("Invalid pValue: ", pValue)
             INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
             continue
 
         if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
-            print("Invalid fc: ", foldChange)
             INVALID_ARROW.styleReactionElements(metabMap, reactionId)
             continue