PKG-INFO

-Metadata-Version: 1.1
+Metadata-Version: 2.1
 Name: pyBigWig
-Version: 0.3.11
+Version: 0.3.12
 Summary: A package for accessing bigWig files using libBigWig
 Home-page: https://github.com/dpryan79/pyBigWig
 Author: Devon P. Ryan
 Author-email: ryan@ie-freiburg.mpg.de
 License: UNKNOWN
 Download-URL: https://github.com/dpryan79/pyBigWig/tarball/0.3.11
-Description-Content-Type: UNKNOWN
 Description: UNKNOWN
 Keywords: bioinformatics,bigWig,bigBed
 Platform: UNKNOWN
+Provides-Extra: numpy input

debian/changelog

+pybigwig (0.3.12-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Diane Trout <diane@ghic.org>  Mon, 15 Oct 2018 21:30:28 -0700
+
 pybigwig (0.3.11-1) unstable; urgency=medium
 
   * New upstream release.

debian/control

@@ -13,7 +13,9 @@ Build-Depends: debhelper (>= 11),
                python3-all-dev,
                python3-numpy,
                python3-setuptools
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
+Vcs-Git: https://salsa.debian.org/med-team/pybigwig.git
+Vcs-Browser: https://salsa.debian.org/med-team/pybigwig
 Section: science
 Homepage: https://github.com/dpryan79/pyBigWig
 

debian/tests/control

@@ -4,7 +4,7 @@ Test-Command: set -e
  ; $py test.py
  ; cd ..
  ; done
-Depends: python-pybigwig
+Depends: python-pybigwig, python-all
 
 Test-Command: set -e
  ; for py in $(py3versions -r 2>/dev/null)
@@ -12,4 +12,4 @@ Test-Command: set -e
  ; $py test.py
  ; cd ..
  ; done
-Depends: python3-pybigwig
+Depends: python3-pybigwig, python3-all

pyBigWig.c

@@ -7,6 +7,7 @@
 #include "numpy/npy_common.h"
 #include "numpy/halffloat.h"
 #include "numpy/ndarrayobject.h"
+#include "numpy/arrayscalars.h"
 
 int lsize = NPY_SIZEOF_LONG;
 
@@ -79,6 +80,52 @@ error:
     return 0;
 };
 
+long getNumpyL(PyObject *obj) {
+    short s;
+    int i;
+    long l;
+    long long ll;
+    unsigned short us;
+    unsigned int ui;
+    unsigned long ul;
+    unsigned long long ull;
+    
+    if(!PyArray_IsIntegerScalar(obj)) {
+        PyErr_SetString(PyExc_RuntimeError, "Received non-Integer scalar type for conversion to long!\n");
+        return 0;
+    }
+
+    if(PyArray_IsScalar(obj, Short)) {
+        s = ((PyShortScalarObject *)obj)->obval;
+        l = s;
+    } else if(PyArray_IsScalar(obj, Int)) {
+        i = ((PyLongScalarObject *)obj)->obval;
+        l = i;
+    } else if(PyArray_IsScalar(obj, Long)) {
+        l = ((PyLongScalarObject *)obj)->obval;
+    } else if(PyArray_IsScalar(obj, LongLong)) {
+        ll = ((PyLongScalarObject *)obj)->obval;
+        l = ll;
+    } else if(PyArray_IsScalar(obj, UShort)) {
+        us = ((PyLongScalarObject *)obj)->obval;
+        l = us;
+    } else if(PyArray_IsScalar(obj, UInt)) {
+        ui = ((PyLongScalarObject *)obj)->obval;
+        l = ui;
+    } else if(PyArray_IsScalar(obj, ULong)) {
+        ul = ((PyLongScalarObject *)obj)->obval;
+        l = ul;
+    } else if(PyArray_IsScalar(obj, ULongLong)) {
+        ull = ((PyLongScalarObject *)obj)->obval;
+        l = ull;
+    } else {
+        PyErr_SetString(PyExc_RuntimeError, "Received unknown scalar type for conversion to long!\n");
+        return 0;
+    }
+
+    return l;
+}
+
 //Raises an exception on error, which should be checked
 float getNumpyF(PyArrayObject *obj, Py_ssize_t i) {
     int dtype;
@@ -324,7 +371,7 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw
     unsigned long startl = 0, endl = -1;
     static char *kwd_list[] = {"chrom", "start", "end", "type", "nBins", "exact", NULL};
     char *chrom, *type = "mean";
-    PyObject *ret, *exact = Py_False;
+    PyObject *ret, *exact = Py_False, *starto = NULL, *endo = NULL;
     int i, nBins = 1;
     errno = 0; //In the off-chance that something elsewhere got an error and didn't clear it...
 
@@ -338,7 +385,7 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw
         return NULL;
     }
 
-    if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|kksiO", kwd_list, &chrom, &startl, &endl, &type, &nBins, &exact)) {
+    if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|OOsiO", kwd_list, &chrom, &starto, &endo, &type, &nBins, &exact)) {
         PyErr_SetString(PyExc_RuntimeError, "You must supply at least a chromosome!");
         return NULL;
     }
@@ -347,6 +394,43 @@ static PyObject *pyBwGetStats(pyBigWigFile_t *self, PyObject *args, PyObject *kw
     if(!nBins) nBins = 1; //For some reason, not specifying this overrides the default!
     if(!type) type = "mean";
     tid = bwGetTid(bw, chrom);
+
+    if(starto) {
+#ifdef WITHNUMPY
+        if(PyArray_IsScalar(starto, Integer)) {
+            startl = (long) getNumpyL(starto);
+        } else 
+#endif
+        if(PyLong_Check(starto)) {
+            startl = PyLong_AsLong(starto);
+#if PY_MAJOR_VERSION < 3
+        } else if(PyInt_Check(starto)) {
+            startl = PyInt_AsLong(starto);
+#endif
+        } else {
+            PyErr_SetString(PyExc_RuntimeError, "The start coordinate must be a number!");
+            return NULL;
+        }
+    }
+
+    if(endo) {
+#ifdef WITHNUMPY
+        if(PyArray_IsScalar(endo, Integer)) {
+            endl = (long) getNumpyL(endo);
+        } else 
+#endif
+        if(PyLong_Check(endo)) {
+            endl = PyLong_AsLong(endo);
+#if PY_MAJOR_VERSION < 3
+        } else if(PyInt_Check(endo)) {
+            endl = PyInt_AsLong(endo);
+#endif
+        } else {
+            PyErr_SetString(PyExc_RuntimeError, "The end coordinate must be a number!");
+            return NULL;
+        }
+    }
+
     if(endl == (unsigned long) -1 && tid != (uint32_t) -1) endl = bw->cl->len[tid];
     if(tid == (uint32_t) -1 || startl > end || endl > end) {
         PyErr_SetString(PyExc_RuntimeError, "Invalid interval bounds!");
@@ -412,7 +496,7 @@ static PyObject *pyBwGetValues(pyBigWigFile_t *self, PyObject *args) {
     uint32_t start, end = -1, tid;
     unsigned long startl, endl;
     char *chrom;
-    PyObject *ret;
+    PyObject *ret, *starto = NULL, *endo = NULL;
     bwOverlappingIntervals_t *o;
 
     if(!bw) {
@@ -429,20 +513,54 @@ static PyObject *pyBwGetValues(pyBigWigFile_t *self, PyObject *args) {
     static char *kwd_list[] = {"chrom", "start", "end", "numpy", NULL};
     PyObject *outputNumpy = Py_False;
 
-    if(!PyArg_ParseTupleAndKeywords(args, kwds, "skk|O", kwd_list, &chrom, &startl, &endl, &outputNumpy)) {
+    if(!PyArg_ParseTupleAndKeywords(args, kwds, "sOO|O", kwd_list, &chrom, &starto, &endo, &outputNumpy)) {
 #else
-    if(!PyArg_ParseTuple(args, "skk", &chrom, &startl, &endl)) {
+    if(!PyArg_ParseTuple(args, "sOO", &chrom, &starto, &endo)) {
 #endif
         PyErr_SetString(PyExc_RuntimeError, "You must supply a chromosome, start and end position.\n");
         return NULL;
     }
 
     tid = bwGetTid(bw, chrom);
+
+#ifdef WITHNUMPY
+    if(PyArray_IsScalar(starto, Integer)) {
+        startl = (long) getNumpyL(starto);
+    } else
+#endif
+    if(PyLong_Check(starto)) {
+        startl = PyLong_AsLong(starto);
+#if PY_MAJOR_VERSION < 3
+    } else if(PyInt_Check(starto)) {
+        startl = PyInt_AsLong(starto);
+#endif
+    } else {
+        PyErr_SetString(PyExc_RuntimeError, "The start coordinate must be a number!");
+        return NULL;
+    }
+
+#ifdef WITHNUMPY
+    if(PyArray_IsScalar(endo, Integer)) {
+        endl = (long) getNumpyL(endo);
+    } else
+#endif
+    if(PyLong_Check(endo)) {
+        endl = PyLong_AsLong(endo);
+#if PY_MAJOR_VERSION < 3
+    } else if(PyInt_Check(endo)) {
+        endl = PyInt_AsLong(endo);
+#endif
+    } else {
+        PyErr_SetString(PyExc_RuntimeError, "The end coordinate must be a number!");
+        return NULL;
+    }
+
     if(endl == (unsigned long) -1 && tid != (uint32_t) -1) endl = bw->cl->len[tid];
     if(tid == (uint32_t) -1 || startl > end || endl > end) {
         PyErr_SetString(PyExc_RuntimeError, "Invalid interval bounds!");
         return NULL;
     }
+
     start = (uint32_t) startl;
     end = (uint32_t) endl;
     if(end <= start || end > bw->cl->len[tid] || start >= end) {
@@ -496,7 +614,7 @@ static PyObject *pyBwGetIntervals(pyBigWigFile_t *self, PyObject *args, PyObject
     static char *kwd_list[] = {"chrom", "start", "end", NULL};
     bwOverlappingIntervals_t *intervals = NULL;
     char *chrom;
-    PyObject *ret;
+    PyObject *ret, *starto = NULL, *endo = NULL;
 
     if(!bw) {
         PyErr_SetString(PyExc_RuntimeError, "The bigWig file handle is not opened!");
@@ -508,7 +626,7 @@ static PyObject *pyBwGetIntervals(pyBigWigFile_t *self, PyObject *args, PyObject
         return NULL;
     }
 
-    if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|kk", kwd_list, &chrom, &startl, &endl)) {
+    if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|OO", kwd_list, &chrom, &starto, &endo)) {
         PyErr_SetString(PyExc_RuntimeError, "You must supply at least a chromosome.\n");
         return NULL;
     }
@@ -520,6 +638,43 @@ static PyObject *pyBwGetIntervals(pyBigWigFile_t *self, PyObject *args, PyObject
         PyErr_SetString(PyExc_RuntimeError, "Invalid interval bounds!");
         return NULL;
     }
+
+    if(starto) {
+#ifdef WITHNUMPY
+        if(PyArray_IsScalar(starto, Integer)) {
+            startl = (long) getNumpyL(starto);
+        } else
+#endif
+        if(PyLong_Check(starto)) {
+            startl = PyLong_AsLong(starto);
+#if PY_MAJOR_VERSION < 3
+        } else if(PyInt_Check(starto)) {
+            startl = PyInt_AsLong(starto);
+#endif
+        } else {
+            PyErr_SetString(PyExc_RuntimeError, "The start coordinate must be a number!");
+            return NULL;
+        }
+    }
+
+    if(endo) {
+#ifdef WITHNUMPY
+        if(PyArray_IsScalar(endo, Integer)) {
+            endl = (long) getNumpyL(endo);
+        } else
+#endif
+        if(PyLong_Check(endo)) {
+            endl = PyLong_AsLong(endo);
+#if PY_MAJOR_VERSION < 3
+        } else if(PyInt_Check(endo)) {
+            endl = PyInt_AsLong(endo);
+#endif
+        } else {
+            PyErr_SetString(PyExc_RuntimeError, "The end coordinate must be a number!");
+            return NULL;
+        }
+    }
+
     start = (uint32_t) startl;
     end = (uint32_t) endl;
     if(end <= start || end > bw->cl->len[tid] || start >= end) {
@@ -1548,7 +1703,7 @@ static PyObject *pyBBGetEntries(pyBigWigFile_t *self, PyObject *args, PyObject *
     unsigned long startl, endl;
     char *chrom;
     static char *kwd_list[] = {"chrom", "start", "end", "withString", NULL};
-    PyObject *ret, *t;
+    PyObject *ret, *t, *starto = NULL, *endo = NULL;
     PyObject *withStringPy = Py_True;
     int withString = 1;
     bbOverlappingEntries_t *o;
@@ -1563,12 +1718,45 @@ static PyObject *pyBBGetEntries(pyBigWigFile_t *self, PyObject *args, PyObject *
         return NULL;  
     }
 
-    if(!PyArg_ParseTupleAndKeywords(args, kwds, "skk|O", kwd_list, &chrom, &startl, &endl, &withStringPy)) {
+    if(!PyArg_ParseTupleAndKeywords(args, kwds, "sOO|O", kwd_list, &chrom, &starto, &endo, &withStringPy)) {
         PyErr_SetString(PyExc_RuntimeError, "You must supply a chromosome, start and end position.\n");
         return NULL;
     }
 
     tid = bwGetTid(bw, chrom);
+
+#ifdef WITHNUMPY
+    if(PyArray_IsScalar(starto, Integer)) {
+        startl = (long) getNumpyL(starto);
+    } else
+#endif
+    if(PyLong_Check(starto)) {
+        startl = PyLong_AsLong(starto);
+#if PY_MAJOR_VERSION < 3
+    } else if(PyInt_Check(starto)) {
+        startl = PyInt_AsLong(starto);
+#endif
+    } else {
+        PyErr_SetString(PyExc_RuntimeError, "The start coordinate must be a number!");
+        return NULL;
+    }
+
+#ifdef WITHNUMPY
+    if(PyArray_IsScalar(endo, Integer)) {
+        endl = (long) getNumpyL(endo);
+    } else
+#endif
+    if(PyLong_Check(endo)) {
+        endl = PyLong_AsLong(endo);
+#if PY_MAJOR_VERSION < 3
+    } else if(PyInt_Check(endo)) {
+        endl = PyInt_AsLong(endo);
+#endif
+    } else {
+        PyErr_SetString(PyExc_RuntimeError, "The end coordinate must be a number!");
+        return NULL;
+    }
+
     if(endl == (unsigned long) -1 && tid != (uint32_t) -1) endl = bw->cl->len[tid];
     if(tid == (uint32_t) -1 || startl > end || endl > end) {
         PyErr_SetString(PyExc_RuntimeError, "Invalid interval bounds!");

pyBigWig.h

@@ -2,7 +2,7 @@
 #include <structmember.h>
 #include "bigWig.h"
 
-#define pyBigWigVersion "0.3.11"
+#define pyBigWigVersion "0.3.12"
 
 typedef struct {
     PyObject_HEAD

pyBigWigTest/test.py

@@ -3,6 +3,7 @@ import tempfile
 import os
 import sys
 import hashlib
+import numpy as np
 
 class TestRemote():
     fname = "http://raw.githubusercontent.com/dpryan79/pyBigWig/master/pyBigWigTest/test.bw"
@@ -28,14 +29,17 @@ class TestRemote():
         assert(bw.stats("1", 0, 3) == [0.2000000054637591])
         assert(bw.stats("1", 0, 3, type="max") == [0.30000001192092896])
         assert(bw.stats("1",99,200, type="max", nBins=2) == [1.399999976158142, 1.5])
+        assert(bw.stats("1",np.int64(99), np.int64(200), type="max", nBins=2) == [1.399999976158142, 1.5])
         assert(bw.stats("1") == [1.3351851569281683])
 
     def doValues(self, bw):
         assert(bw.values("1", 0, 3) == [0.10000000149011612, 0.20000000298023224, 0.30000001192092896])
+        assert(bw.values("1", np.int64(0), np.int64(3)) == [0.10000000149011612, 0.20000000298023224, 0.30000001192092896])
         #assert(bw.values("1", 0, 4) == [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, 'nan'])
 
     def doIntervals(self, bw):
         assert(bw.intervals("1", 0, 3) == ((0, 1, 0.10000000149011612), (1, 2, 0.20000000298023224), (2, 3, 0.30000001192092896)))
+        assert(bw.intervals("1", np.int64(0), np.int64(3)) == ((0, 1, 0.10000000149011612), (1, 2, 0.20000000298023224), (2, 3, 0.30000001192092896)))
         assert(bw.intervals("1") == ((0, 1, 0.10000000149011612), (1, 2, 0.20000000298023224), (2, 3, 0.30000001192092896), (100, 150, 1.399999976158142), (150, 151, 1.5)))
 
     def doSum(self, bw):
@@ -161,7 +165,6 @@ class TestRemote():
         os.remove(oname)
 
     def doWriteNumpy(self):
-        import numpy as np
         ofile = tempfile.NamedTemporaryFile(delete=False)
         oname = ofile.name
         ofile.close()
@@ -237,6 +240,8 @@ class TestBigBed():
         o = bb.entries('chr1',10000000,10020000)
         expected = [(10009333, 10009640, '61035\t130\t-\t0.026\t0.42\t404'), (10014007, 10014289, '61047\t136\t-\t0.029\t0.42\t404'), (10014373, 10024307, '61048\t630\t-\t5.420\t0.00\t2672399')]
         assert(o == expected)
+        o = bb.entries('chr1',np.int64(10000000),np.int64(10020000))
+        assert(o == expected)
         bb.close()
 
 class TestNumpy():

setup.py

@@ -15,7 +15,7 @@ srcs = [x for x in
     glob.glob("libBigWig/*.c")]
 srcs.append("pyBigWig.c")
 
-libs=["m", "z", "curl"]
+libs=["m", "z"]
 
 # do not link to python on mac, see https://github.com/deeptools/pyBigWig/issues/58
 if 'dynamic_lookup' not in (sysconfig.get_config_var('LDSHARED') or ''):
@@ -34,6 +34,7 @@ additional_libs = [sysconfig.get_config_var("LIBDIR"), sysconfig.get_config_var(
 defines = []
 try:
     foo, _ = subprocess.Popen(['curl-config', '--libs'], stdout=subprocess.PIPE).communicate()
+    libs.append("curl")
 except:
     foo = ''
     defines.append(('NOCURL', None))
@@ -61,7 +62,7 @@ module1 = Extension('pyBigWig',
                     include_dirs = include_dirs)
 
 setup(name = 'pyBigWig',
-       version = '0.3.11',
+       version = '0.3.12',
        description = 'A package for accessing bigWig files using libBigWig',
        author = "Devon P. Ryan",
        author_email = "ryan@ie-freiburg.mpg.de",