added prefix argument two motifGrammar and EmptyBackground scripts

kundajelab · Jan 22, 2018 · a6f0bd0 · a6f0bd0
1 parent 2083d7e
commit a6f0bd0
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/scripts/emptyBackground.py b/scripts/emptyBackground.py
@@ -7,6 +7,7 @@
 
 def do(options):
     outputFileName_core = util.addArguments("EmptyBackground", [
+                                                 util.ArgumentToAdd(options.prefix, "prefix"),
                                                  util.ArgumentToAdd(options.seqLength, "seqLength")
                                                  ,util.ArgumentToAdd(options.numSeqs, "numSeqs")
                                                  ])
@@ -15,10 +16,12 @@ def do(options):
         , embedders=[]
     );
     sequenceSet = sn.GenerateSequenceNTimes(embedInBackground, options.numSeqs)
-    sn.printSequences(outputFileName_core+".simdata", sequenceSet, includeFasta=True, includeEmbeddings=True)
+    sn.printSequences(outputFileName_core+".simdata", sequenceSet, includeFasta=True, includeEmbeddings=True,
+                      prefix=options.prefix)
 
 if __name__=="__main__":
     parser = argparse.ArgumentParser();
+    parser.add_argument("--prefix")
     parser.add_argument("--seqLength", type=int, required=True)
     parser.add_argument("--numSeqs", type=int, required=True)
     options = parser.parse_args()

diff --git a/scripts/motifGrammarSimulation.py b/scripts/motifGrammarSimulation.py
@@ -25,7 +25,7 @@ def motifGrammarSimulation(options):
     seqLength = options.seqLength
     numSeq = options.numSeq
     generationSetting = options.generationSetting
-    outputFileName = "motifGrammarSimulation_"+generationSetting+("_bestHit" if bestHit else "")
+    outputFileName = "motifGrammarSimulation_"+("prefix-"+options.prefix+"_" if options.prefix is not None else "")+generationSetting+("_bestHit" if bestHit else "")
     if (generationSetting is not generationSettings.singleMotif2):
         outputFileName+="_motif1-"+motifName1
     if (generationSetting is not generationSettings.singleMotif1):
@@ -89,11 +89,13 @@ def motifGrammarSimulation(options):
 
     sequenceSet = synthetic.GenerateSequenceNTimes(embedInBackground, numSeq)
     synthetic.printSequences(outputFileName, sequenceSet,
-                             includeFasta=True, includeEmbeddings=True)
+                             includeFasta=True, includeEmbeddings=True,
+                             prefix=options.prefix)
 
 if __name__ == "__main__":
     import argparse
     parser = argparse.ArgumentParser()
+    parser.add_argument("--prefix")
     parser.add_argument("--pathToMotifs",
         default=simdna.ENCODE_MOTIFS_PATH)
     parser.add_argument("--motifName1", required=True)

diff --git a/scripts_test/test_empty_background_script.sh b/scripts_test/test_empty_background_script.sh
@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 
-emptyBackground.py --seqLength 200 --numSeqs 10
+emptyBackground.py --prefix empty --seqLength 200 --numSeqs 10
diff --git a/scripts_test/test_motif_grammar_simulation_script.sh b/scripts_test/test_motif_grammar_simulation_script.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 #variable spacing
-motifGrammarSimulation.py --motifName1 TAL1_known1 --motifName2 GATA_disc2 --seqLength 200 --numSeq 10 --generationSetting twoMotifsVariableSpacing --fixedSpacingOrMinSpacing 1 --maxSpacing 5
+motifGrammarSimulation.py --prefix testprefix --motifName1 TAL1_known1 --motifName2 GATA_disc2 --seqLength 200 --numSeq 10 --generationSetting twoMotifsVariableSpacing --fixedSpacingOrMinSpacing 1 --maxSpacing 5
 
 #variable spacing best hit
 motifGrammarSimulation.py --motifName1 TAL1_known1 --motifName2 GATA_disc2 --bestHit --seqLength 200 --numSeq 100 --generationSetting twoMotifsVariableSpacing --fixedSpacingOrMinSpacing 1 --maxSpacing 5