Merge pull request #1257 from lldelisle/fix_error_handling

Fix error handling + cases where with bigwigAverage with more than 2 bigwigs
deeptools · Sep 27, 2023 · d56b016 · d56b016
2 parents aca3def + f0c8223
commit d56b016
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Showing 2 changed files with 18 additions and 4 deletions.
diff --git a/deeptools/test/test_bigwigAverage.py b/deeptools/test/test_bigwigAverage.py
@@ -69,3 +69,15 @@ def test_bigwigAverageWithScale():
     expected = ['3R\t0\t50\t0\n', '3R\t50\t100\t0.25\n', '3R\t100\t150\t0.75\n', '3R\t150\t200\t1\n']
     assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
     unlink(outfile)
+
+
+def test_bigwigAverageThree():
+    outfile = '/tmp/result.bg'
+    args = "--bigwigs {} {} {} -o {} --outFileFormat bedgraph --scaleFactors 0.75:0.75:.75".format(BIGWIG_A, BIGWIG_A, BIGWIG_B, outfile).split()
+    bwAve.main(args)
+    _foo = open(outfile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    expected = ['3R\t0\t50\t0\n', '3R\t50\t100\t0.25\n', '3R\t100\t150\t0.75\n', '3R\t150\t200\t1\n']
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(outfile)
diff --git a/deeptools/writeBedGraph_bam_and_bw.py b/deeptools/writeBedGraph_bam_and_bw.py
@@ -23,7 +23,7 @@ def getCoverageFromBigwig(bigwigHandle, chrom, start, end, tileSize,
                           missingDataAsZero=False):
     try:
         coverage = np.asarray(bigwigHandle.values(chrom, start, end))
-    except TypeError:
+    except RuntimeError:
         # this error happens when chromosome
         # is not into the bigwig file
         return []
@@ -170,7 +170,7 @@ def writeBedGraph(
         chromNamesAndSize, __ = getCommonChrNames(bamHandles, verbose=verbose)
     else:
         genomeChunkLength = int(10e6)
-        cCommon = []
+        cCommon_number = {}
         chromNamesAndSize = {}
         for fileName, fileFormat in bamOrBwFileList:
             if fileFormat == 'bigwig':
@@ -180,7 +180,7 @@ def writeBedGraph(
 
             for chromName, size in list(fh.chroms().items()):
                 if chromName in chromNamesAndSize:
-                    cCommon.append(chromName)
+                    cCommon_number[chromName] += 1
                     if chromNamesAndSize[chromName] != size:
                         print("\nWARNING\n"
                               "Chromosome {} length reported in the "
@@ -193,14 +193,16 @@ def writeBedGraph(
                             chromNamesAndSize[chromName], size)
                 else:
                     chromNamesAndSize[chromName] = size
+                    cCommon_number[chromName] = 1
             fh.close()
 
         # get the list of common chromosome names and sizes
         if len(bamOrBwFileList) == 1:
             chromNamesAndSize = [(k, v) for k, v in chromNamesAndSize.items()]
         else:
             chromNamesAndSize = [(k, v) for k, v in chromNamesAndSize.items()
-                                 if k in cCommon]
+                                 if k in cCommon_number and
+                                 cCommon_number[k] == len(bamOrBwFileList)]
 
     if region:
         # in case a region is used, append the tilesize