diff spring_minz.py @ 27:e34da554d415 draft

"planemo upload commit f12d400ea7827bb7d6b2ef31eb7f38e555bd053f-dirty"

--- a/spring_minz.py	Sat Oct 31 22:21:11 2020 +0000
+++ b/spring_minz.py	Sat Oct 31 22:46:10 2020 +0000
@@ -40,6 +40,7 @@
                     inputs=inputs,
                     inputPath=inputPath,
                     crossReference=crossReference,
+                    idLength=args.idlength,
                     minScore=args.minscore,
                     logFile=logFile,
                     interactions=interactions)
@@ -53,6 +54,7 @@
                         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)
@@ -61,15 +63,15 @@
             output_file.write("%s\t%s\t%s\t%s\n" % (entry["targetName"], entry["inputName"], entry["minZ"], entry["minInfo"]))
     logFile.close()
 
-def matchScores(targetFile, targetName, inputs, inputPath, crossReference, minScore, logFile, interactions):
-    targetTop, targetHits = getTemplateScores(targetFile, minScore)
+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)
     else:
         print ("Loaded target scores from `%s`." % targetFile)
         for inputName in inputs:
             inputFile = "%s/%s" % (inputPath, inputName)
-            inputTop, inputHits = getTemplateScores(inputFile, minScore)
+            inputTop, inputHits = getTemplateScores(inputFile, minScore, idLength)
             minZ = 0
             minInfo = ""
             for t in targetHits:
@@ -92,16 +94,17 @@
                 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):
+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[4:10]
+                    templateId = line[4:idLength]
                     templateScore = float(line[57:63])
                     if templateScore > minScore:
                         if topTemplate is None:
@@ -119,5 +122,6 @@
     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)
     args = parser.parse_args()
     main(args)
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