Plotfingerprint na to nan (#1002)

* change "NA" occurences in plotFingerprint.py to proper numpy.NAN

* update expected plotFingerprint output in galaxy from NA to nan

deeptools/plotFingerprint.py

@@ -202,10 +202,10 @@ def getCHANCE(args, idx, mat):
     """
     # Get the index of the reference sample
     if args.JSDsample not in args.bamfiles:
-        return ["NA", "NA", "NA"]
+        return [np.NAN, np.NAN, np.NAN]
     refIdx = args.bamfiles.index(args.JSDsample)
     if refIdx == idx:
-        return ["NA", "NA", "NA"]
+        return [np.NAN, np.NAN, np.NAN]
 
     subMatrix = np.copy(mat[:, [idx, refIdx]])
     subMatrix[np.isnan(subMatrix)] = 0
@@ -271,10 +271,10 @@ def getJSD(args, idx, mat):
 
     # Get the index of the reference sample
     if args.JSDsample not in args.bamfiles:
-        return "NA"
+        return np.NAN
     refIdx = args.bamfiles.index(args.JSDsample)
     if refIdx == idx:
-        return "NA"
+        return np.NAN
 
     # These will hold the coverage histograms
     chip = np.zeros(MAXLEN, dtype=np.int)
@@ -338,7 +338,7 @@ def signalAndBinDist(x):
 
     if abs(sum(PMFinput) - 1) > 0.01 or abs(sum(PMFchip) - 1) > 0.01:
         sys.stderr.write("Warning: At least one PMF integral is significantly different from 1! The JSD will not be returned")
-        return "NA"
+        return np.NAN
 
     # Compute the JSD from the PMFs
     M = (PMFinput + PMFchip) / 2.0

galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular

@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	NA	0.26900449806812143	NA	NA	NA
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	nan	0.26900449806812143	nan	nan	nan
 bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	0.0	0.26900449806812143	0	0	0