Implement #816

deeptools/bigwigCompare.py

@@ -61,6 +61,12 @@ def parse_arguments(args=None):
                         type=float,
                         required=False)
 
+    parser.add_argument('--skipZeroOverZero',
+                        help='Skip bins where BOTH BAM files lack coverage. '
+                        'This is determined BEFORE any applicable pseudocount '
+                        'is added.',
+                        action='store_true')
+
     parser.add_argument('--operation',
                         help='The default is to output the log2ratio of the '
                         'two samples. The reciprocal ratio returns the '
@@ -159,6 +165,7 @@ def main(args=None):
         blackListFileName=args.blackListFileName,
         verbose=args.verbose,
         numberOfProcessors=args.numberOfProcessors,
+        skipZeroOverZero=args.skipZeroOverZero,
         format=args.outFileFormat,
         smoothLength=False,
         missingDataAsZero=not args.skipNonCoveredRegions,

deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py

@@ -62,6 +62,18 @@ def test_bigwigCompare_skipnas():
     unlink(outfile)
 
 
+def test_bigwigCompare_skipZeroOverZero():
+    outfile = '/tmp/result.bg"'
+    args = "-b1 {} -b2 {} -o {} --skipZeroOverZero --pseudocount 1 3 --outFileFormat bedgraph".format(BIGWIG_A, BIGWIG_A, outfile).split()
+    bwComp.main(args)
+    _foo = open(outfile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    expected = ['3R\t100\t200\t-1\n']
+    assert resp == expected, "{} != {}".format(resp, expected)
+    unlink(outfile)
+
+
 def test_multiBigwigSummary():
     outfile = '/tmp/result.bg'
     args = "bins -b {} {} --binSize 50 -o {}".format(BIGWIG_A, BIGWIG_B, outfile).split()

deeptools/writeBedGraph_bam_and_bw.py

@@ -45,7 +45,7 @@ def writeBedGraph_wrapper(args):
 def writeBedGraph_worker(
         chrom, start, end, tileSize, defaultFragmentLength,
         bamOrBwFileList, func, funcArgs, extendPairedEnds=True, smoothLength=0,
-        missingDataAsZero=False, fixed_step=False):
+        skipZeroOverZero=False, missingDataAsZero=False, fixed_step=False):
     r"""
     Writes a bedgraph having as base a number of bam files.
 
@@ -102,6 +102,10 @@ def writeBedGraph_worker(
                              "files. Remove this chromosome from the bigwig file "
                              "to continue".format(chrom))
 
+        if skipZeroOverZero and np.sum(tileCoverage) == 0:
+            previousValue = None
+            continue
+
         value = func(tileCoverage, funcArgs)
 
         if fixed_step:
@@ -147,7 +151,7 @@ def writeBedGraph(
         bamOrBwFileList, outputFileName, fragmentLength,
         func, funcArgs, tileSize=25, region=None, blackListFileName=None, numberOfProcessors=1,
         format="bedgraph", extendPairedEnds=True, missingDataAsZero=False,
-        smoothLength=0, fixed_step=False, verbose=False):
+        skipZeroOverZero=False, smoothLength=0, fixed_step=False, verbose=False):
     r"""
     Given a list of bamfiles, a function and a function arguments,
     this method writes a bedgraph file (or bigwig) file
@@ -206,7 +210,7 @@ def writeBedGraph(
 
     res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
                                func, funcArgs, extendPairedEnds, smoothLength,
-                               missingDataAsZero, fixed_step),
+                               skipZeroOverZero, missingDataAsZero, fixed_step),
                               writeBedGraph_wrapper,
                               chromNamesAndSize,
                               genomeChunkLength=genomeChunkLength,

galaxy/wrapper/bamCompare.xml

@@ -164,11 +164,7 @@
                 <expand macro="read_processing_options" />
 
                 <expand macro="skipNAs" />
-                <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
-                    help="Skip bins where BOTH files lack coverage.">
-                    <option value="" selected="true">No</option>
-                    <option value="--skipZeroOverZero">Yes, skip them.</option>
-                </param>
+                <expand macro="skipZeroOverZero" />
 
                 <param argument="--ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"

galaxy/wrapper/bigwigCompare.xml

@@ -28,6 +28,7 @@
             #if $advancedOpt.showAdvancedOpt == "yes":
 
               $advancedOpt.skipNAs
+              $advancedOpt.skipZeroOverZero
               --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
               --binSize $advancedOpt.binSize
 
@@ -95,6 +96,7 @@
                     help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
 
                 <expand macro="skipNAs" />
+                <expand macro="skipZeroOverZero" />
                 <expand macro="scaleFactors" />
                 <expand macro="plotTitle" />
                 <expand macro="blacklist" />

galaxy/wrapper/deepTools_macros.xml

@@ -650,6 +650,14 @@ is vital to you, select Yes below.">
                  (default: False)" />
     </xml>
 
+    <xml name="skipZeroOverZero">
+        <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
+            help="Skip bins where BOTH files lack coverage.">
+            <option value="" selected="true">No</option>
+            <option value="--skipZeroOverZero">Yes, skip them.</option>
+        </param>
+    </xml>
+
     <xml name="exactScaling">
         <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
             label="Compute an exact scaling factor"

setup.py

@@ -86,8 +86,8 @@ def openREADME():
         "scipy >= 0.17.0",
         "matplotlib >= 2.1.2",
         "pysam >= 0.14.0",
-        "numpydoc >=0.5",
-        "pyBigWig >=0.2.1",
+        "numpydoc >= 0.5",
+        "pyBigWig >= 0.2.1",
         "py2bit >= 0.2.0",
         "plotly >= 2.0.0",
         "deeptoolsintervals >= 0.1.7"