Plot fingerprint: return proper nans

README.md

@@ -2,6 +2,7 @@
 [![Build Status](https://dev.azure.com/dpryan79/dpryan79/_apis/build/status/deeptools.deepTools?branchName=master)](https://dev.azure.com/dpryan79/dpryan79/_build/latest?definitionId=1&branchName=master)
 [![Documentation Status](https://readthedocs.org/projects/deeptools/badge/)](http://deeptools.readthedocs.org/) [![PyPI Version](https://img.shields.io/pypi/v/deeptools.svg?style=plastic)](https://pypi.org/project/deepTools/) 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/deeptools/README.html)
+[![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=deeptools_multi_bam_summary)
 
 ## User-friendly tools for exploring deep-sequencing data
 

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