Codebase list pybigwig / 7c65191
Import upstream version 0.3.18 Debian Janitor 2 years ago
9 changed file(s) with 148 addition(s) and 35 deletion(s). Raw diff Collapse all Expand all
+13
-0
.environmentLinux.yaml less more
0 name: foo
1 channels:
2 - conda-forge
3 - bioconda
4 - default
5 dependencies:
6 - gcc_linux-64
7 - curl
8 - zlib
9 - python 3.8
10 - pip
11 - numpy
12 - nose
+19
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.github/workflows/build.yml less more
0 on: pull_request
1 jobs:
2 testLinux:
3 name: TestLinux
4 runs-on: "ubuntu-latest"
5 defaults:
6 run:
7 shell: bash -l {0}
8 steps:
9 - uses: actions/checkout@v2
10 - uses: conda-incubator/setup-miniconda@v2
11 with:
12 activate-environment: foo
13 environment-file: .environmentLinux.yaml
14 python-version: 3.8
15 auto-activate-base: false
16 - run: |
17 pip install .
18 nosetests -sv
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.github/workflows/pypi.yml less more
0 name: pypi
1 on: [push]
2 jobs:
3 pypi:
4 name: upload to pypi
5 runs-on: ubuntu-latest
6 steps:
7 - uses: actions/checkout@v1
8 - name: Setup conda
9 if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
10 run: |
11 curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
12 bash miniconda.sh -b -p $HOME/miniconda
13 export PATH="$HOME/miniconda/bin:$PATH"
14 hash -r
15 conda config --set always_yes yes --set changeps1 no
16 - name: create env
17 if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
18 run: |
19 export PATH=$HOME/miniconda/bin:$PATH
20 conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine numpy libcurl curl zlib
21 - name: sdist
22 if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
23 run: |
24 export PATH=$HOME/miniconda/bin:$PATH
25 source activate foo
26 rm -f dist/*
27 python setup.py sdist
28 - name: upload
29 if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
30 env:
31 TWINE_USERNAME: "__token__"
32 TWINE_PASSWORD: ${{ secrets.pypi_password }}
33 run: |
34 export PATH=$HOME/miniconda/bin:$PATH
35 source activate foo
36 twine upload dist/*
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-11
.travis.yml less more
0 language: python
1 python:
2 - "3.5"
3 - "3.6"
4 install:
5 - pip install numpy && python ./setup.py install
6 matrix:
7 include:
8 - python: 3.7
9 dist: xenial
10 script: nosetests -sv
+11
-3
README.md less more
66 =================
77
88 * [Installation](#installation)
9 * [Requirements](#requirements)
910 * [Usage](#usage)
1011 * [Load the extension](#load-the-extension)
1112 * [Open a bigWig or bigBed file](#open-a-bigwig-or-bigbed-file)
3334
3435 or with conda
3536
36 conda install pybigwig -c bioconda
37
38 Note that libcurl (and the `curl-config` command) are required for installation. This is typically already installed on many Linux and OSX systems (if you install with conda then this will happen automatically).
37 conda install pybigwig -c conda-forge -c bioconda
38
39 ## Requirements
40
41 The follow non-python requirements must be installed:
42
43 - libcurl (and the `curl-config` config)
44 - zlib
45
46 The headers and libraries for these are required.
3947
4048 # Usage
4149 Basic usage is as follows:
+46
-19
pyBigWig.c less more
196196
197197 //Return 1 if there are any entries at all
198198 int hasEntries(bigWigFile_t *bw) {
199 if(bw->hdr->nBasesCovered > 0) return 1;
199 if(bw->hdr->indexOffset != 0) return 1; // No index, no entries pyBigWig issue #111
200 //if(bw->hdr->nBasesCovered > 0) return 1; // Sometimes headers are broken
200201 return 0;
201202 }
202203
377378 double *val;
378379 uint32_t start, end = -1, tid;
379380 unsigned long startl = 0, endl = -1;
380 static char *kwd_list[] = {"chrom", "start", "end", "type", "nBins", "exact", NULL};
381 static char *kwd_list[] = {"chrom", "start", "end", "type", "nBins", "exact", "numpy", NULL};
381382 char *chrom, *type = "mean";
382383 PyObject *ret, *exact = Py_False, *starto = NULL, *endo = NULL;
384 PyObject *outputNumpy = Py_False;
383385 int i, nBins = 1;
384386 errno = 0; //In the off-chance that something elsewhere got an error and didn't clear it...
385387
398400 return NULL;
399401 }
400402
401 if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|OOsiO", kwd_list, &chrom, &starto, &endo, &type, &nBins, &exact)) {
403 if(!PyArg_ParseTupleAndKeywords(args, kwds, "s|OOsiOO", kwd_list, &chrom, &starto, &endo, &type, &nBins, &exact, &outputNumpy)) {
402404 PyErr_SetString(PyExc_RuntimeError, "You must supply at least a chromosome!");
403405 return NULL;
404406 }
463465
464466 //Return a list of None if there are no entries at all
465467 if(!hasEntries(bw)) {
466 ret = PyList_New(nBins);
467 for(i=0; i<nBins; i++) {
468 Py_INCREF(Py_None);
469 PyList_SetItem(ret, i, Py_None);
470 }
468 #ifdef WITHNUMPY
469 if(outputNumpy == Py_True) {
470 val = malloc(sizeof(double)*nBins);
471 for(i=0; i<nBins; i++) {
472 val[i] = NPY_NAN;
473 }
474 npy_intp len = nBins;
475 ret = PyArray_SimpleNewFromData(1, &len, NPY_FLOAT64, (void *) val);
476 //This will break if numpy ever stops using malloc!
477 PyArray_ENABLEFLAGS((PyArrayObject*) ret, NPY_ARRAY_OWNDATA);
478 } else {
479 #endif
480 ret = PyList_New(nBins);
481 for(i=0; i<nBins; i++) {
482 Py_INCREF(Py_None);
483 PyList_SetItem(ret, i, Py_None);
484 }
485 #ifdef WITHNUMPY
486 }
487 #endif
471488 return ret;
472489 }
473490
483500 return NULL;
484501 }
485502
486 ret = PyList_New(nBins);
487 for(i=0; i<nBins; i++) {
488 if(isnan(val[i])) {
489 Py_INCREF(Py_None);
490 PyList_SetItem(ret, i, Py_None);
491 } else {
492 PyList_SetItem(ret, i, PyFloat_FromDouble(val[i]));
493 }
494 }
495 free(val);
496
503 #ifdef WITHNUMPY
504 if(outputNumpy == Py_True) {
505 npy_intp len = nBins;
506 ret = PyArray_SimpleNewFromData(1, &len, NPY_FLOAT64, (void *) val);
507 //This will break if numpy ever stops using malloc!
508 PyArray_ENABLEFLAGS((PyArrayObject*) ret, NPY_ARRAY_OWNDATA);
509 } else {
510 #endif
511 ret = PyList_New(nBins);
512 for(i=0; i<nBins; i++) {
513 if(isnan(val[i])) {
514 Py_INCREF(Py_None);
515 PyList_SetItem(ret, i, Py_None);
516 } else {
517 PyList_SetItem(ret, i, PyFloat_FromDouble(val[i]));
518 }
519 }
520 free(val);
521 #ifdef WITHNUMPY
522 }
523 #endif
497524 return ret;
498525 }
499526
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-1
pyBigWig.h less more
11 #include <structmember.h>
22 #include "bigWig.h"
33
4 #define pyBigWigVersion "0.3.17"
4 #define pyBigWigVersion "0.3.18"
55
66 typedef struct {
77 PyObject_HEAD
+20
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pyBigWigTest/test.py less more
307307
308308 bw.close()
309309 os.remove("/tmp/delete.bw")
310
311 def testNumpyValues(self):
312 if pyBigWig.numpy == 0:
313 return 0
314 import numpy as np
315
316 fname = "http://raw.githubusercontent.com/dpryan79/pyBigWig/master/pyBigWigTest/test.bw"
317 bw = pyBigWig.open(fname, "r")
318
319 assert np.allclose(
320 bw.values("1", 0, 20, numpy=True),
321 np.array(bw.values("1", 0, 20), dtype=np.float32),
322 equal_nan=True
323 )
324
325 assert np.allclose(
326 bw.stats("1", 0, 20, "mean", 5, numpy=True),
327 np.array(bw.stats("1", 0, 20, "mean", 5), dtype=np.float64),
328 equal_nan=True
329 )
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setup.py less more
6161 include_dirs = include_dirs)
6262
6363 setup(name = 'pyBigWig',
64 version = '0.3.17',
64 version = '0.3.18',
6565 description = 'A package for accessing bigWig files using libBigWig',
6666 author = "Devon P. Ryan",
6767 author_email = "ryan@ie-freiburg.mpg.de",