diff spring_minz.py @ 39:172398348efd draft

"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"

--- a/spring_minz.py	Wed Nov 25 17:38:24 2020 +0000
+++ b/spring_minz.py	Fri Jan 22 15:50:27 2021 +0000
@@ -1,18 +1,23 @@
 #! /usr/bin/env python3
 import argparse
-import os
+
+from spring_package.Utilities import getCrossReference, getTemplates
 
 
 def main(args):
-    logFile = open(args.log, 'a+')
+    minScore = args.minscore
+    logFile = open(args.log, 'w')
     targets = list()
     targetPath = args.targetpath.rstrip("/")
+    hhrResults = dict()
     with open(args.targetlist) as file:
         for line in file:
             name = line.strip()
             targets.append(name)
-    print("Loaded %s target names from `%s`." % (len(targets),
-          args.targetlist))
+    print("Loaded %s target names from `%s`." % (len(targets), args.targetlist))
+    for targetName in targets:
+        targetFile = "%s/%s" % (targetPath, targetName)
+        hhrResults[targetName] = getTemplates(targetFile, minScore)
     if args.inputlist:
         inputs = list()
         inputPath = args.inputpath.rstrip("/")
@@ -20,48 +25,26 @@
             for line in file:
                 name = line.strip()
                 inputs.append(name)
-        print("Loaded %s input names from `%s`." % (len(inputs),
-              args.inputlist))
+        print("Loaded %s input names from `%s`." % (len(inputs), args.inputlist))
+        for inputName in inputs:
+            if inputName not in hhrResults:
+                inputFile = "%s/%s" % (inputPath, inputName)
+                hhrResults[inputName] = getTemplates(inputFile, minScore)
     else:
         inputs = targets
-        inputPath = targetPath
-    crossReference = dict()
-    with open(args.crossreference) as file:
-        for line in file:
-            columns = line.split()
-            core = columns[0]
-            partner = columns[-1]
-            if core not in crossReference:
-                crossReference[core] = []
-            crossReference[core].append(partner)
-    print("Loaded cross reference from `%s`." % args.crossreference)
+    print("Loaded hhr results for %s entries." % len(hhrResults.keys()))
+    crossReference = getCrossReference(args.cross)
+    print("Loaded cross reference from `%s`." % args.cross)
     interactions = dict()
     for targetName in targets:
-        targetFile = "%s/%s" % (targetPath, targetName)
-        matchScores(targetFile=targetFile,
+        matchScores(hhrResults=hhrResults,
                     targetName=targetName,
                     inputs=inputs,
-                    inputPath=inputPath,
                     crossReference=crossReference,
-                    idLength=args.idlength,
                     minScore=args.minscore,
                     logFile=logFile,
                     interactions=interactions)
-    if args.inputlist:
-        for inputName in inputs:
-            inputDirectory = inputPath
-            inputFile = "%s/%s" % (inputDirectory, inputName)
-            matchScores(targetFile=inputFile,
-                        targetName=inputName,
-                        inputs=targets,
-                        inputPath=targetPath,
-                        crossReference=crossReference,
-                        minScore=args.minscore,
-                        idLength=args.idlength,
-                        logFile=logFile,
-                        interactions=interactions)
-    interactions = sorted(interactions.values(), key=lambda item: item["minZ"],
-                          reverse=True)
+    interactions = sorted(interactions.values(), key=lambda item: item["minZ"], reverse=True)
     with open(args.output, 'w') as output_file:
         for entry in interactions:
             output_file.write("%s\t%s\t%s\t%s\n" % (entry["targetName"],
@@ -70,61 +53,39 @@
     logFile.close()
 
 
-def matchScores(targetFile, targetName, inputs, inputPath, crossReference,
-                minScore, idLength, logFile, interactions):
-    targetTop, targetHits = getTemplateScores(targetFile, minScore, idLength)
-    if not targetHits:
-        print("No targets found `%s`" % targetFile)
+def matchScores(hhrResults, targetName, inputs, crossReference, minScore, logFile, interactions):
+    if targetName not in hhrResults:
+        print("Target not found `%s`" % targetName)
     else:
-        print("Loaded target scores from `%s`." % targetFile)
+        targetTop, targetHits = hhrResults[targetName]
+        print("Evaluating %s." % targetName)
+        logFile.write("Evaluating %s.\n" % targetName)
+        logFile.flush()
         for inputName in inputs:
-            inputFile = "%s/%s" % (inputPath, inputName)
-            inputTop, inputHits = getTemplateScores(inputFile,
-                                                    minScore, idLength)
-            minZ = 0
-            minInfo = ""
-            for t in targetHits:
-                if t in crossReference:
-                    partners = crossReference[t]
-                    for p in partners:
-                        if p in inputHits:
-                            score = min(targetHits[t], inputHits[p])
-                            if score > minZ:
-                                minZ = score
-                                minInfo = "%s\t%s\t%s\t%s" % (targetTop,
-                                                              inputTop, t, p)
-            if minZ > minScore:
-                if targetName > inputName:
-                    interactionKey = "%s_%s" % (targetName, inputName)
-                else:
-                    interactionKey = "%s_%s" % (inputName, targetName)
-                if interactionKey in interactions:
-                    if interactions[interactionKey]["minZ"] >= minZ:
-                        continue
-                interactions[interactionKey] = dict(targetName=targetName,
-                                                    inputName=inputName,
-                                                    minZ=minZ, minInfo=minInfo)
-                logFile.write("Interaction between %s and %s [min-Z: %s].\n" % 
-                              (targetName, inputName, minZ))
-
-
-def getTemplateScores(hhrFile, minScore, idLength):
-    result = dict()
-    topTemplate = None
-    idLength = idLength + 4
-    if os.path.isfile(hhrFile):
-        with open(hhrFile) as file:
-            for index, line in enumerate(file):
-                if index > 8:
-                    if not line.strip():
-                        break
-                    templateId = line[4:idLength]
-                    templateScore = float(line[57:63])
-                    if templateScore > minScore:
-                        if topTemplate is None:
-                            topTemplate = templateId
-                        result[templateId] = templateScore
-    return topTemplate, result
+            if inputName in hhrResults:
+                inputTop, inputHits = hhrResults[inputName]
+                minZ = 0
+                minInfo = ""
+                for t in targetHits:
+                    if t in crossReference:
+                        partners = crossReference[t]["partners"]
+                        for p in partners:
+                            if p in inputHits:
+                                score = min(targetHits[t], inputHits[p])
+                                if score > minZ:
+                                    minZ = score
+                                    minInfo = "%s\t%s\t%s\t%s" % (targetTop, inputTop, t, p)
+                if minZ > minScore:
+                    if targetName > inputName:
+                        interactionKey = "%s_%s" % (targetName, inputName)
+                    else:
+                        interactionKey = "%s_%s" % (inputName, targetName)
+                    if interactionKey in interactions:
+                        if interactions[interactionKey]["minZ"] >= minZ:
+                            continue
+                    interactions[interactionKey] = dict(targetName=targetName,
+                                                        inputName=inputName,
+                                                        minZ=minZ, minInfo=minInfo)
 
 
 if __name__ == "__main__":
@@ -133,10 +94,9 @@
     parser.add_argument('-tp', '--targetpath', help='Directory containing `hhr` files', required=True)
     parser.add_argument('-il', '--inputlist', help='Text file containing identifiers.', required=False)
     parser.add_argument('-ip', '--inputpath', help='Directory containing `hhr` files', required=False)
-    parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True)
+    parser.add_argument('-c', '--cross', help='PDB Cross Reference', required=True)
     parser.add_argument('-o', '--output', help='Output file containing min-Z scores', required=True)
     parser.add_argument('-l', '--log', help='Log file', required=True)
-    parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10)
-    parser.add_argument('-idx', '--idlength', help='Length of identifier in reference', type=int, default=6)
+    parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=25)
     args = parser.parse_args()
     main(args)