Merge pull request #224 from pachterlab/devel

Release version 0.27.3 → 0.28.0

.github/workflows/ci.yml

@@ -5,7 +5,7 @@ on: [push]
 jobs:
   check-code:
     name: Check code quality
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout branch
         uses: actions/checkout@master
@@ -19,10 +19,10 @@ jobs:
       - name: Check code quality
         run: make check
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9 ]
+        python: [3.7, 3.8, 3.9 ]
         os: [ubuntu-20.04]
     name: Test on Python ${{ matrix.python }}
     steps:

.github/workflows/release.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   release-to-pypi:
     name: Release to Pypi
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout branch
         uses: actions/checkout@master

.gitignore

@@ -63,6 +63,9 @@ instance/
 # Scrapy stuff:
 .scrapy
 
+# Mac stuff:
+.DS_Store
+
 # Sphinx documentation
 docs/_build/
 docs/api/
@@ -104,4 +107,5 @@ venv.bak/
 # mypy
 .mypy_cache/
 .DS_Store
-.vscode/
+.vscode/
+.Rhistory

README.md

@@ -1,6 +1,6 @@
 # kb-python
-![github version](https://img.shields.io/badge/Version-0.27.3-informational)
-[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.27.3/)
+![github version](https://img.shields.io/badge/Version-0.28.0-informational)
+[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.28.0/)
 ![python versions](https://img.shields.io/pypi/pyversions/kb_python)
 ![status](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/pachterlab/kb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/pachterlab/kb_python)
@@ -59,10 +59,14 @@ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa <GENOME> <GENOME_ANNOTATION>
 	- For example, the zebrafish genome annotation file is hosted by [ensembl](https://uswest.ensembl.org/Danio_rerio/Info/Index) and can be downloaded [here](http://ftp.ensembl.org/pub/release-107/gtf/danio_rerio/Danio_rerio.GRCz11.107.gtf.gz)
 - **Note:** The latest genome annotation and genome file for every species on ensembl can be found with the [`gget`](https://github.com/pachterlab/gget) command-line tool.
 
+Prebuilt indices are available at https://github.com/pachterlab/kallisto-transcriptome-indices
+
 #### Examples
 ```bash
-# Index the zebrafish transcriptome genome.fa.gz annotation.gtf.gz
+# Index the transcriptome from genome FASTA (genome.fa.gz) and GTF (annotation.gtf.gz)
 $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa genome.fa.gz annotation.gtf.gz
+# An example for downloading a prebuilt reference for mouse
+$ kb ref -d mouse -i index.idx -g t2g.txt
 ```
 ---
 ### `kb count`: pseudoalign and count reads
@@ -93,9 +97,9 @@ The `kb info` command prints out package information including the version of `k
 
 ```bash
 $ kb info
-kb_python 0.27.3 ...
-kallisto: 0.48.0 ...
-bustools: 0.41.0 ...
+kb_python 0.28.0 ...
+kallisto: 0.50.1 ...
+bustools: 0.43.1 ...
 ...
 ```
 ---

dev-requirements.txt

@@ -7,5 +7,5 @@ sphinx>=3.3.1
 sphinx-autoapi>=1.5.1
 sphinx_rtd_theme>=0.5.0
 twine>=2.0.0
-wheel==0.34.2
+wheel==0.38.1
 yapf==0.30.0

docs/conf.py

@@ -24,7 +24,7 @@
 author = 'Kyung Hoi (Joseph) Min'
 
 # The full version, including alpha/beta/rc tags
-release = '0.27.3'
+release = '0.28.0'
 master_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -6,7 +6,7 @@
 Welcome to kb-python's documentation!
 =====================================
 
-This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.27.3``.
+This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.28.0``.
 For user documentation and tutorials, please go to `kallisto | bustools <https://www.kallistobus.tools/>`_.
 
 Development Prerequisites

kb_python/__init__.py

@@ -1 +1 @@
-__version__ = '0.27.3'
+__version__ = '0.28.0'

kb_python/bins/darwin/m1/bustools/LICENSE

@@ -0,0 +1,25 @@
+BSD 2-Clause License
+
+Copyright (c) 2018, BUStools
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

kb_python/bins/darwin/m1/kallisto/license.txt

@@ -0,0 +1,25 @@
+BSD 2-Clause License
+
+Copyright (c) 2017, Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

kb_python/config.py

@@ -9,6 +9,9 @@
 
 PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
 PLATFORM = platform.system().lower()
+CPU = ''
+if PLATFORM == 'darwin' and platform.processor().lower() == 'arm':
+    CPU = 'm1'
 BINS_DIR = os.path.join(PACKAGE_PATH, 'bins')
 COMPILED_DIR = os.path.join(BINS_DIR, 'compiled')
 
@@ -32,7 +35,7 @@ def get_provided_kallisto_path() -> Optional[str]:
         Path to the binary, `None` if not found
     """
     bin_filename = 'kallisto.exe' if PLATFORM == 'windows' else 'kallisto'
-    path = os.path.join(BINS_DIR, PLATFORM, 'kallisto', bin_filename)
+    path = os.path.join(BINS_DIR, PLATFORM, CPU, 'kallisto', bin_filename)
     if not os.path.isfile(path):
         return None
     return path
@@ -45,7 +48,7 @@ def get_provided_bustools_path() -> Optional[str]:
         Path to the binary, `None` if not found
     """
     bin_filename = 'bustools.exe' if PLATFORM == 'windows' else 'bustools'
-    path = os.path.join(BINS_DIR, PLATFORM, 'bustools', bin_filename)
+    path = os.path.join(BINS_DIR, PLATFORM, CPU, 'bustools', bin_filename)
     if not os.path.isfile(path):
         return None
     return path
@@ -143,6 +146,9 @@ class Technology(NamedTuple):
     Technology(
         'SMARTSEQ3', 'Smart-seq3', ngs.chemistry.get_chemistry('smartseq3')
     ),
+    Technology(
+        'STORMSEQ', 'STORM-seq', ngs.chemistry.get_chemistry('stormseq')
+    ),
     Technology(
         'BDWTA', 'BD Rhapsody', ngs.chemistry.get_chemistry('bd rhapsody')
     ),

kb_python/constants.py

@@ -19,6 +19,7 @@
 BUS_CDNA_PREFIX = 'spliced'
 BUS_INTRON_PREFIX = 'unspliced'
 ECMAP_FILENAME = 'matrix.ec'
+GENE_NAMES_FILENAME = 'genes.names.txt'
 TXNAMES_FILENAME = 'transcripts.txt'
 KB_INFO_FILENAME = 'kb_info.json'
 KALLISTO_INFO_FILENAME = 'run_info.json'
@@ -31,6 +32,8 @@
 GENE_NAME = 'gene'
 FEATURE_NAME = 'feature'
 TRANSCRIPT_NAME = 'transcript'
+GENOMEBAM_FILENAME = 'pseudoalignments.bam'
+GENOMEBAM_INDEX_FILENAME = 'pseudoalignments.bam.bai'
 
 UNFILTERED_COUNTS_DIR = 'counts_unfiltered'
 FILTERED_COUNTS_DIR = 'counts_filtered'
@@ -46,6 +49,7 @@
 FLENS_FILENAME = 'flens.txt'
 BATCH_FILENAME = 'batch.txt'
 ABUNDANCE_GENE_FILENAME = 'matrix.abundance.gene.mtx'
+ABUNDANCE_GENE_NAMES_FILENAME = 'matrix.abundance.gene.names.mtx'
 ABUNDANCE_GENE_TPM_FILENAME = 'matrix.abundance.gene.tpm.mtx'
 ABUNDANCE_FILENAME = 'matrix.abundance.mtx'
 ABUNDANCE_TPM_FILENAME = 'matrix.abundance.tpm.mtx'
@@ -71,3 +75,6 @@
 FILTERED_CODE = 'filtered'
 UNFILTERED_CODE = 'unfiltered'
 PROJECT_CODE = 'p'
+
+# Loom
+VELOCYTO_LOOM_NAMES = 'CellID,Gene'