New upstream version 0.2.1
Andreas Tille
3 years ago
0 | 0 | Metadata-Version: 1.2 |
1 | 1 | Name: pauvre |
2 | Version: 0.1924 | |
2 | Version: 0.2.1 | |
3 | 3 | Summary: Tools for plotting Oxford Nanopore and other long-read data. |
4 | 4 | Home-page: https://github.com/conchoecia/pauvre |
5 | 5 | Author: Darrin Schultz |
6 | 6 | Author-email: dts@ucsc.edu |
7 | License: GPLv3 | |
7 | License: UNKNOWN | |
8 | 8 | Description: |
9 | 9 | 'pauvre' is a package for plotting Oxford Nanopore and other long read data. |
10 | 10 | The name means 'poor' in French, a play on words to the oft-used 'pore' prefix |
16 | 16 | Classifier: Development Status :: 2 - Pre-Alpha |
17 | 17 | Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) |
18 | 18 | Classifier: Programming Language :: Python :: 3 |
19 | Classifier: Programming Language :: Python :: 3.5 | |
19 | Classifier: Programming Language :: Python :: 3.6 | |
20 | Classifier: Programming Language :: Python :: 3.7 | |
20 | 21 | Classifier: Operating System :: POSIX :: Linux |
21 | 22 | Classifier: Topic :: Scientific/Engineering :: Bio-Informatics |
22 | 23 | Classifier: Intended Audience :: Science/Research |
23 | Requires: python (>3.0) | |
24 | Provides: pauvre | |
25 | 24 | Requires-Python: >=3 |
22 | 22 | parsimonius rotation to display the synteny of all the input |
23 | 23 | genomes with the fewest crossings-over. Input is one `.gff` file |
24 | 24 | per circular genome and one directory of gene alignments. |
25 | ||
26 | ## Updates: | |
27 | - 20200215 - v0.1.924 - Made some minor updates to work with python 3.7 and the latest version of pandas, | |
28 | - 20171130 - v0.1.86 - some changes by @wdecoster to integrate `pauvre` into [nanoplot](https://github.com/wdecoster/NanoPlot), | |
29 | as well as some formatting changes that *may* make `pauvre` work better with python2.7. Adding Travis-CI functionality. | |
30 | - 20171025 - v0.1.83 - added some changes to make marginplot interface | |
31 | with @wdecoster's [nanoPlot](https://github.com/wdecoster/NanoPlot) | |
32 | package, and made `pauvre stats` only output data tables for | |
33 | filtered reads. `pauvre stats` also now has the `--filt_maxlen`, | |
34 | `--filt_maxqual`, `--filt_minlen`, and `--filt_minqual` options. | |
35 | - 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window. | |
36 | [See below for a demonstration.](#filter-reads-and-adjust-viewing-window) I added the following options: | |
37 | ||
38 | ``` | |
39 | --filt_maxlen FILT_MAXLEN | |
40 | This sets the max read length filter reads. | |
41 | --filt_maxqual FILT_MAXQUAL | |
42 | This sets the max mean read quality to filter reads. | |
43 | --filt_minlen FILT_MINLEN | |
44 | This sets the min read length to filter reads. | |
45 | --filt_minqual FILT_MINQUAL | |
46 | This sets the min mean read quality to filter reads. | |
47 | --plot_maxlen PLOT_MAXLEN | |
48 | Sets the maximum viewing area in the length dimension. | |
49 | --plot_maxqual PLOT_MAXQUAL | |
50 | Sets the maximum viewing area in the quality | |
51 | dimension. | |
52 | --plot_minlen PLOT_MINLEN | |
53 | Sets the minimum viewing area in the length dimension. | |
54 | --plot_minqual PLOT_MINQUAL | |
55 | Sets the minimum viewing area in the quality | |
56 | dimension. | |
57 | ``` | |
58 | - 20171014 - uploading information on `pauvre redwood` and `pauvre synteny` usage. | |
59 | - 20171012 - made `pauvre stats` more consistently produce useful histograms. | |
60 | `pauvre stats` now also calculates some statistics for different size ranges. | |
61 | - 20170529 - added automatic scaling to the input fastq file. It | |
62 | scales to show the highest read quality and the top 99th percentile | |
63 | of reads by length. | |
64 | 25 | |
65 | 26 | # Requirements |
66 | 27 |
377 | 377 | min_plot_qual, max_plot_qual, min_plot_length, max_plot_length), |
378 | 378 | file=stderr) |
379 | 379 | # Print image(s) |
380 | if kwargs["BASENAME"] is None and not kwargs["path"] is None: | |
381 | file_base = kwargs["BASENAME"] | |
382 | elif kwargs["BASENAME"] is None: | |
380 | if kwargs["BASENAME"] is None: | |
383 | 381 | file_base = opath.splitext(opath.basename(kwargs["fastq"]))[0] |
384 | 382 | else: |
385 | 383 | file_base = kwargs["BASENAME"] |
4 | 4 | def update_rcParams(): |
5 | 5 | # This mpl style is from the UCSC BME163 class. |
6 | 6 | rcParams.update({ |
7 | 'font.size' : 8.0 , | |
8 | 'font.sans-serif' : 'Arial' , | |
9 | 'xtick.major.size' : 2 , | |
10 | 'xtick.major.width' : 0.75 , | |
11 | 'xtick.labelsize' : 8.0 , | |
12 | 'xtick.direction' : 'out' , | |
13 | 'ytick.major.size' : 2 , | |
14 | 'ytick.major.width' : 0.75 , | |
15 | 'ytick.labelsize' : 8.0 , | |
16 | 'ytick.direction' : 'out' , | |
17 | 'xtick.major.pad' : 2 , | |
18 | 'xtick.minor.pad' : 2 , | |
19 | 'ytick.major.pad' : 2 , | |
20 | 'ytick.minor.pad' : 2 , | |
21 | 'savefig.dpi' : 601 , | |
22 | 'axes.linewidth' : 0.75 , | |
23 | 'text.usetex' : False , | |
24 | 'text.latex.unicode' : False }) | |
7 | 'font.size' : 8.0 , | |
8 | 'font.sans-serif' : 'Arial' , | |
9 | 'xtick.major.size' : 2 , | |
10 | 'xtick.major.width' : 0.75 , | |
11 | 'xtick.labelsize' : 8.0 , | |
12 | 'xtick.direction' : 'out' , | |
13 | 'ytick.major.size' : 2 , | |
14 | 'ytick.major.width' : 0.75 , | |
15 | 'ytick.labelsize' : 8.0 , | |
16 | 'ytick.direction' : 'out' , | |
17 | 'xtick.major.pad' : 2 , | |
18 | 'xtick.minor.pad' : 2 , | |
19 | 'ytick.major.pad' : 2 , | |
20 | 'ytick.minor.pad' : 2 , | |
21 | 'savefig.dpi' : 601 , | |
22 | 'axes.linewidth' : 0.75 , | |
23 | 'text.usetex' : False , | |
24 | "image.composite_image": False , | |
25 | "pdf.fonttype" : 42, | |
26 | "ps.fonttype" : 42 }) | |
27 |
702 | 702 | end = time.time() |
703 | 703 | print(end - start) |
704 | 704 | # Print image(s) |
705 | ifargs.BASENAME is None: | |
705 | if args.BASENAME is None: | |
706 | 706 | file_base = "redwood" |
707 | 707 | else: |
708 | 708 | file_base = args.BASENAME |
0 | 0 | Metadata-Version: 1.2 |
1 | 1 | Name: pauvre |
2 | Version: 0.1924 | |
2 | Version: 0.2.1 | |
3 | 3 | Summary: Tools for plotting Oxford Nanopore and other long-read data. |
4 | 4 | Home-page: https://github.com/conchoecia/pauvre |
5 | 5 | Author: Darrin Schultz |
6 | 6 | Author-email: dts@ucsc.edu |
7 | License: GPLv3 | |
7 | License: UNKNOWN | |
8 | 8 | Description: |
9 | 9 | 'pauvre' is a package for plotting Oxford Nanopore and other long read data. |
10 | 10 | The name means 'poor' in French, a play on words to the oft-used 'pore' prefix |
16 | 16 | Classifier: Development Status :: 2 - Pre-Alpha |
17 | 17 | Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3) |
18 | 18 | Classifier: Programming Language :: Python :: 3 |
19 | Classifier: Programming Language :: Python :: 3.5 | |
19 | Classifier: Programming Language :: Python :: 3.6 | |
20 | Classifier: Programming Language :: Python :: 3.7 | |
20 | 21 | Classifier: Operating System :: POSIX :: Linux |
21 | 22 | Classifier: Topic :: Scientific/Engineering :: Bio-Informatics |
22 | 23 | Classifier: Intended Audience :: Science/Research |
23 | Requires: python (>3.0) | |
24 | Provides: pauvre | |
25 | 24 | Requires-Python: >=3 |
0 | 0 | #!/usr/bin/env python3 |
1 | 1 | # -*- coding: utf-8 -*- |
2 | 2 | |
3 | # pauvre | |
3 | # pauvre | |
4 | 4 | # Copyright (c) 2016-2020 Darrin T. Schultz. |
5 | 5 | # |
6 | 6 | # This file is part of pauvre. |
27 | 27 | |
28 | 28 | version_py = os.path.join(os.path.dirname(__file__), 'pauvre', 'version.py') |
29 | 29 | version = open(version_py).read().strip().split('=')[-1].replace('"', '').strip() |
30 | print(version) | |
31 | 30 | |
32 | 31 | |
33 | 32 | setup(name='pauvre', |
34 | requires=['python (>3.0)'], | |
35 | 33 | version=version, |
36 | 34 | description='Tools for plotting Oxford Nanopore and other long-read data.', |
37 | 35 | long_description=""" |
41 | 39 | python 2. You can visit the gitub page for more detailed information here: |
42 | 40 | https://github.com/conchoecia/pauvre |
43 | 41 | """, |
44 | ||
45 | 42 | url='https://github.com/conchoecia/pauvre', |
46 | 43 | author='Darrin Schultz', |
47 | 44 | author_email='dts@ucsc.edu', |
49 | 46 | 'Development Status :: 2 - Pre-Alpha', |
50 | 47 | 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', |
51 | 48 | 'Programming Language :: Python :: 3', |
52 | 'Programming Language :: Python :: 3.5', | |
49 | 'Programming Language :: Python :: 3.6', | |
50 | 'Programming Language :: Python :: 3.7', | |
53 | 51 | 'Operating System :: POSIX :: Linux', |
54 | 52 | 'Topic :: Scientific/Engineering :: Bio-Informatics', |
55 | 'Intended Audience :: Science/Research' | |
53 | 'Intended Audience :: Science/Research', | |
56 | 54 | ], |
57 | license='GPLv3', | |
58 | provides=['pauvre'], | |
59 | packages=find_packages() + ['scripts'], | |
55 | packages=find_packages(), | |
60 | 56 | python_requires='>=3', |
61 | 57 | install_requires=[ |
62 | 58 | "matplotlib >= 2.0.2", |
64 | 60 | "pandas >= 0.20.1", |
65 | 61 | "numpy >= 1.12.1", |
66 | 62 | "scipy", |
67 | "sklearn" | |
63 | "scikit-learn", | |
68 | 64 | ], |
69 | 65 | entry_points={ |
70 | 66 | 'console_scripts': ['pauvre=pauvre.pauvre_main:main'], |