diff --git a/PKG-INFO b/PKG-INFO index 043b040..99c527a 100644 --- a/PKG-INFO +++ b/PKG-INFO @@ -1,11 +1,11 @@ Metadata-Version: 1.2 Name: pauvre -Version: 0.1924 +Version: 0.2.1 Summary: Tools for plotting Oxford Nanopore and other long-read data. Home-page: https://github.com/conchoecia/pauvre Author: Darrin Schultz Author-email: dts@ucsc.edu -License: GPLv3 +License: UNKNOWN Description: 'pauvre' is a package for plotting Oxford Nanopore and other long read data. The name means 'poor' in French, a play on words to the oft-used 'pore' prefix @@ -17,10 +17,9 @@ Classifier: Development Status :: 2 - Pre-Alpha Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) Classifier: Programming Language :: Python :: 3 -Classifier: Programming Language :: Python :: 3.5 +Classifier: Programming Language :: Python :: 3.6 +Classifier: Programming Language :: Python :: 3.7 Classifier: Operating System :: POSIX :: Linux Classifier: Topic :: Scientific/Engineering :: Bio-Informatics Classifier: Intended Audience :: Science/Research -Requires: python (>3.0) -Provides: pauvre Requires-Python: >=3 diff --git a/README.md b/README.md index f16c7b2..0122fc3 100644 --- a/README.md +++ b/README.md @@ -23,45 +23,6 @@ parsimonius rotation to display the synteny of all the input genomes with the fewest crossings-over. Input is one `.gff` file per circular genome and one directory of gene alignments. - -## Updates: -- 20200215 - v0.1.924 - Made some minor updates to work with python 3.7 and the latest version of pandas, -- 20171130 - v0.1.86 - some changes by @wdecoster to integrate `pauvre` into [nanoplot](https://github.com/wdecoster/NanoPlot), - as well as some formatting changes that *may* make `pauvre` work better with python2.7. Adding Travis-CI functionality. -- 20171025 - v0.1.83 - added some changes to make marginplot interface - with @wdecoster's [nanoPlot](https://github.com/wdecoster/NanoPlot) - package, and made `pauvre stats` only output data tables for - filtered reads. `pauvre stats` also now has the `--filt_maxlen`, - `--filt_maxqual`, `--filt_minlen`, and `--filt_minqual` options. -- 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window. - [See below for a demonstration.](#filter-reads-and-adjust-viewing-window) I added the following options: - -``` - --filt_maxlen FILT_MAXLEN - This sets the max read length filter reads. - --filt_maxqual FILT_MAXQUAL - This sets the max mean read quality to filter reads. - --filt_minlen FILT_MINLEN - This sets the min read length to filter reads. - --filt_minqual FILT_MINQUAL - This sets the min mean read quality to filter reads. - --plot_maxlen PLOT_MAXLEN - Sets the maximum viewing area in the length dimension. - --plot_maxqual PLOT_MAXQUAL - Sets the maximum viewing area in the quality - dimension. - --plot_minlen PLOT_MINLEN - Sets the minimum viewing area in the length dimension. - --plot_minqual PLOT_MINQUAL - Sets the minimum viewing area in the quality - dimension. -``` -- 20171014 - uploading information on `pauvre redwood` and `pauvre synteny` usage. -- 20171012 - made `pauvre stats` more consistently produce useful histograms. - `pauvre stats` now also calculates some statistics for different size ranges. -- 20170529 - added automatic scaling to the input fastq file. It - scales to show the highest read quality and the top 99th percentile - of reads by length. # Requirements diff --git a/pauvre/marginplot.py b/pauvre/marginplot.py index 1c24e57..53da1ae 100644 --- a/pauvre/marginplot.py +++ b/pauvre/marginplot.py @@ -378,9 +378,7 @@ min_plot_qual, max_plot_qual, min_plot_length, max_plot_length), file=stderr) # Print image(s) - if kwargs["BASENAME"] is None and not kwargs["path"] is None: - file_base = kwargs["BASENAME"] - elif kwargs["BASENAME"] is None: + if kwargs["BASENAME"] is None: file_base = opath.splitext(opath.basename(kwargs["fastq"]))[0] else: file_base = kwargs["BASENAME"] diff --git a/pauvre/rcparams.py b/pauvre/rcparams.py index fac7145..89a4b9e 100644 --- a/pauvre/rcparams.py +++ b/pauvre/rcparams.py @@ -5,21 +5,24 @@ def update_rcParams(): # This mpl style is from the UCSC BME163 class. rcParams.update({ - 'font.size' : 8.0 , - 'font.sans-serif' : 'Arial' , - 'xtick.major.size' : 2 , - 'xtick.major.width' : 0.75 , - 'xtick.labelsize' : 8.0 , - 'xtick.direction' : 'out' , - 'ytick.major.size' : 2 , - 'ytick.major.width' : 0.75 , - 'ytick.labelsize' : 8.0 , - 'ytick.direction' : 'out' , - 'xtick.major.pad' : 2 , - 'xtick.minor.pad' : 2 , - 'ytick.major.pad' : 2 , - 'ytick.minor.pad' : 2 , - 'savefig.dpi' : 601 , - 'axes.linewidth' : 0.75 , - 'text.usetex' : False , - 'text.latex.unicode' : False }) + 'font.size' : 8.0 , + 'font.sans-serif' : 'Arial' , + 'xtick.major.size' : 2 , + 'xtick.major.width' : 0.75 , + 'xtick.labelsize' : 8.0 , + 'xtick.direction' : 'out' , + 'ytick.major.size' : 2 , + 'ytick.major.width' : 0.75 , + 'ytick.labelsize' : 8.0 , + 'ytick.direction' : 'out' , + 'xtick.major.pad' : 2 , + 'xtick.minor.pad' : 2 , + 'ytick.major.pad' : 2 , + 'ytick.minor.pad' : 2 , + 'savefig.dpi' : 601 , + 'axes.linewidth' : 0.75 , + 'text.usetex' : False , + "image.composite_image": False , + "pdf.fonttype" : 42, + "ps.fonttype" : 42 }) + diff --git a/pauvre/redwood.py b/pauvre/redwood.py index 277a608..059440d 100644 --- a/pauvre/redwood.py +++ b/pauvre/redwood.py @@ -703,7 +703,7 @@ end = time.time() print(end - start) # Print image(s) - ifargs.BASENAME is None: + if args.BASENAME is None: file_base = "redwood" else: file_base = args.BASENAME diff --git a/pauvre/version.py b/pauvre/version.py index 22ea753..200a6d2 100644 --- a/pauvre/version.py +++ b/pauvre/version.py @@ -1,3 +1,4 @@ # -*- coding: utf-8 -*- -__version__ = "0.1924" +__version__ = "0.2.1" + diff --git a/pauvre.egg-info/PKG-INFO b/pauvre.egg-info/PKG-INFO index 043b040..99c527a 100644 --- a/pauvre.egg-info/PKG-INFO +++ b/pauvre.egg-info/PKG-INFO @@ -1,11 +1,11 @@ Metadata-Version: 1.2 Name: pauvre -Version: 0.1924 +Version: 0.2.1 Summary: Tools for plotting Oxford Nanopore and other long-read data. Home-page: https://github.com/conchoecia/pauvre Author: Darrin Schultz Author-email: dts@ucsc.edu -License: GPLv3 +License: UNKNOWN Description: 'pauvre' is a package for plotting Oxford Nanopore and other long read data. The name means 'poor' in French, a play on words to the oft-used 'pore' prefix @@ -17,10 +17,9 @@ Classifier: Development Status :: 2 - Pre-Alpha Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) Classifier: Programming Language :: Python :: 3 -Classifier: Programming Language :: Python :: 3.5 +Classifier: Programming Language :: Python :: 3.6 +Classifier: Programming Language :: Python :: 3.7 Classifier: Operating System :: POSIX :: Linux Classifier: Topic :: Scientific/Engineering :: Bio-Informatics Classifier: Intended Audience :: Science/Research -Requires: python (>3.0) -Provides: pauvre Requires-Python: >=3 diff --git a/pauvre.egg-info/requires.txt b/pauvre.egg-info/requires.txt index f2e372a..2df747c 100644 --- a/pauvre.egg-info/requires.txt +++ b/pauvre.egg-info/requires.txt @@ -3,4 +3,4 @@ pandas>=0.20.1 numpy>=1.12.1 scipy -sklearn +scikit-learn diff --git a/pauvre.egg-info/top_level.txt b/pauvre.egg-info/top_level.txt index 68ebe9c..57f5848 100644 --- a/pauvre.egg-info/top_level.txt +++ b/pauvre.egg-info/top_level.txt @@ -1,2 +1 @@ pauvre -scripts diff --git a/setup.py b/setup.py index 3da3e10..7e38014 100755 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- -# pauvre +# pauvre # Copyright (c) 2016-2020 Darrin T. Schultz. # # This file is part of pauvre. @@ -28,11 +28,9 @@ version_py = os.path.join(os.path.dirname(__file__), 'pauvre', 'version.py') version = open(version_py).read().strip().split('=')[-1].replace('"', '').strip() -print(version) setup(name='pauvre', - requires=['python (>3.0)'], version=version, description='Tools for plotting Oxford Nanopore and other long-read data.', long_description=""" @@ -42,7 +40,6 @@ python 2. You can visit the gitub page for more detailed information here: https://github.com/conchoecia/pauvre """, - url='https://github.com/conchoecia/pauvre', author='Darrin Schultz', author_email='dts@ucsc.edu', @@ -50,14 +47,13 @@ 'Development Status :: 2 - Pre-Alpha', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', 'Operating System :: POSIX :: Linux', 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Intended Audience :: Science/Research' + 'Intended Audience :: Science/Research', ], - license='GPLv3', - provides=['pauvre'], - packages=find_packages() + ['scripts'], + packages=find_packages(), python_requires='>=3', install_requires=[ "matplotlib >= 2.0.2", @@ -65,7 +61,7 @@ "pandas >= 0.20.1", "numpy >= 1.12.1", "scipy", - "sklearn" + "scikit-learn", ], entry_points={ 'console_scripts': ['pauvre=pauvre.pauvre_main:main'],