Merge pull request #55 from deeptools/fix54

Fix BigWig creation with numpy

Author: dpryan79

.travis.yml

@@ -6,5 +6,5 @@ python:
   - "3.4"
   - "3.5"
   - "3.6"
-install: python ./setup.py install
+install: pip install numpy && python ./setup.py install
 script: nosetests -sv

pyBigWig.c

@@ -119,6 +119,7 @@ float getNumpyF(PyArrayObject *obj, Py_ssize_t i) {
     return 0;
 }
 
+//The calling function needs to free the result
 char *getNumpyStr(PyArrayObject *obj, Py_ssize_t i) {
     char *p , *o = NULL;
     npy_intp stride, j;
@@ -137,7 +138,7 @@ char *getNumpyStr(PyArrayObject *obj, Py_ssize_t i) {
         return o;
     case NPY_UNICODE:
         o = calloc(1, stride/4 + 1);
-        for(j=0; j<stride/4; j++) o[j] = (char) ((uint32_t*)p)[4*j];
+        for(j=0; j<stride/4; j++) o[j] = (char) ((uint32_t*)p)[j];
         return o;
     default:
         PyErr_SetString(PyExc_RuntimeError, "Received unknown data type!\n");
@@ -908,6 +909,7 @@ int canAppend(pyBigWigFile_t *self, int desiredType, PyObject *chroms, PyObject
     PyObject *tmp;
 #ifdef WITHNUMPY
     void *foo;
+    char *chrom;
 #endif
 
     if(self->lastType == -1) return 0;
@@ -925,10 +927,9 @@ int canAppend(pyBigWigFile_t *self, int desiredType, PyObject *chroms, PyObject
         for(i=0; i<sz; i++) {
 #ifdef WITHNUMPY
             if(PyArray_Check(chroms)) {
-                foo = PyArray_GETPTR1((PyArrayObject*)chroms, i);
-                tmp = PyArray_GETITEM((PyArrayObject*)chroms, foo);
-                tid = bwGetTid(bw, PyString_AsString(tmp));
-                Py_DECREF(tmp);
+                chrom = getNumpyStr((PyArrayObject*)chroms, i);
+                tid = bwGetTid(bw, chrom);
+                free(chrom);
             } else {
 #endif
                 tmp = PyList_GetItem(chroms, i);
@@ -1021,10 +1022,7 @@ int PyAddIntervals(pyBigWigFile_t *self, PyObject *chroms, PyObject *starts, PyO
             cchroms[i] = PyString_AsString(PyList_GetItem(chroms, i));
 #ifdef WITHNUMPY
         } else {
-            foo = PyArray_GETPTR1((PyArrayObject*)chroms, i);
-            tmp = PyArray_GETITEM((PyArrayObject*)chroms, foo);
-            cchroms[i] = PyString_AsString(tmp);
-            Py_DECREF(tmp);
+            cchroms[i] = getNumpyStr((PyArrayObject*)chroms, i);
 #endif
         }
         if(PyList_Check(starts)) {
@@ -1058,6 +1056,9 @@ int PyAddIntervals(pyBigWigFile_t *self, PyObject *chroms, PyObject *starts, PyO
         self->lastTid = bwGetTid(bw, cchroms[n-1]);
         self->lastStart = uends[n-1];
     }
+    if(!PyList_Check(chroms)) {
+        for(i=0; i<n; i++) free(cchroms[i]);
+    }
     free(cchroms);
     free(ustarts);
     free(uends);

pyBigWig.h

@@ -2,7 +2,7 @@
 #include <structmember.h>
 #include "bigWig.h"
 
-#define pyBigWigVersion "0.3.9"
+#define pyBigWigVersion "0.3.10"
 
 typedef struct {
     PyObject_HEAD

pyBigWigTest/test.py

@@ -157,18 +157,46 @@ def doWriteEmpty(self):
         #Clean up
         os.remove(oname)
 
+    def doWriteNumpy(self):
+        import numpy as np
+        ofile = tempfile.NamedTemporaryFile(delete=False)
+        oname = ofile.name
+        ofile.close()
+        bw = pyBigWig.open(oname, "w")
+        bw.addHeader([("chr1", 100), ("chr2", 150), ("chr3", 200), ("chr4", 250)])
+        chroms = np.array(["chr1"] * 2 + ["chr2"] * 2 + ["chr3"] * 2 + ["chr4"] * 2)
+        starts = np.array([0, 10, 40, 50, 60, 70, 80, 90], dtype=np.int64)
+        ends = np.array([5, 15, 45, 55, 65, 75, 85, 95], dtype=np.int64)
+        values0 = np.array(np.random.random_sample(8), dtype=np.float64)
+        bw.addEntries(chroms, starts, ends=ends, values=values0)
+        bw.close()
+
+        vals = [(x, y, z) for x, y, z in zip(starts, ends, values0)]
+        bw = pyBigWig.open(oname)
+        assert(bw.chroms() == {'chr1': 100, 'chr2': 150, 'chr3': 200, 'chr4': 250})
+        for idx1, chrom in enumerate(["chr1", "chr2", "chr3", "chr4"]):
+            for idx2, tup in enumerate(bw.intervals(chrom)):
+                assert(tup[0] == starts[2 * idx1 + idx2])
+                assert(tup[1] == ends[2 * idx1 + idx2])
+                assert(np.isclose(tup[2], values0[2 * idx1 + idx2]))
+        bw.close()
+
+        #Clean up
+        os.remove(oname)
+
     def testAll(self):
         bw = self.doOpen()
         self.doChroms(bw)
-        self.doHeader(bw)
-        self.doStats(bw)
-        self.doValues(bw)
-        self.doIntervals(bw)
-        self.doWrite(bw)
         if not self.fname.startswith("http"):
+            self.doHeader(bw)
+            self.doStats(bw)
+            self.doValues(bw)
+            self.doIntervals(bw)
+            self.doWrite(bw)
             self.doOpenWith()
             self.doWrite2()
             self.doWriteEmpty()
+            self.doWriteNumpy()
         bw.close()
 
 class TestLocal():

setup.py

@@ -58,12 +58,12 @@
                     include_dirs = include_dirs)
 
 setup(name = 'pyBigWig',
-       version = '0.3.9',
+       version = '0.3.10',
        description = 'A package for accessing bigWig files using libBigWig',
        author = "Devon P. Ryan",
        author_email = "[email protected]",
        url = "https://github.com/dpryan79/pyBigWig",
-       download_url = "https://github.com/dpryan79/pyBigWig/tarball/0.3.9",
+       download_url = "https://github.com/dpryan79/pyBigWig/tarball/0.3.10",
        keywords = ["bioinformatics", "bigWig", "bigBed"],
        classifier = ["Development Status :: 5 - Production/Stable",
                      "Intended Audience :: Developers",