Commit upstream/latest - python-pauvre

New upstream version 0.2.2 Andreas Tille 2 years ago

5 changed file(s) with 60 addition(s) and 69 deletion(s). Raw diff Collapse all Expand all

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PKG-INFO less more

0	0	Metadata-Version: 1.2
1	1	Name: pauvre
2		Version: 0.2.1
	2	Version: 0.2.2
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

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README.md less more

0	0	[![travis-ci](https://travis-ci.org/conchoecia/pauvre.svg?branch=master)](https://travis-ci.org/conchoecia/pauvre) [![DOI](https://zenodo.org/badge/112774670.svg)](https://zenodo.org/badge/latestdoi/112774670)
1	1
	2	## <a name="started"></a>Getting Started
2	3
3		## pauvre: a plotting package designed for nanopore and PacBio long reads
	4	```
	5	pauvre custommargin -i custom.tsv --ycol length --xcol qual # Custom tsv input
	6	```
4	7
5		This package currently hosts four scripts for plotting and/or printing stats.
	8	## Table of Contents
	9
	10	- [Getting Started](#started)
	11	- [Users' Guide](#uguide)
	12	- [Installation](#installation)
	13	- [Requirements](#reqs)
	14	- [Install Instructions](#install)
	15	- [Usage](#usage)
	16	- [pauvre stats](#stats)
	17	- [pauvre marginplot](#marginplot)
	18	- [Basic Usage](#marginbasic)
	19	- [Plot Adjustments](#marginadjustments)
	20	- [Specialized Options](#marginspecialized)
	21	- [Contributors](#contributors)
	22
	23	## <a name="uguide"></a>Users' Guide
	24
	25	Pauvre is a plotting package originally designed to help QC the length and
	26	quality distribution of Oxford Nanopore or PacBio reads. The main outputs
	27	are marginplots. Now, `pauvre` also hosts other additional data plotting
	28	scripts.
	29
	30	This package currently hosts five scripts for plotting and/or printing stats.
6	31
7	32	- `pauvre marginplot`
8	33	- takes a fastq file as input and outputs a marginal histogram with a heatmap.
	34	- `pauvre custommargin`
	35	- takes a tsv as input and outputs a marginal histogram with custom columns of your choice.
9	36	- `pauvre stats`
10	37	- Takes a fastq file as input and prints out a table of stats, including how many basepairs/reads there are for a length/mean quality cutoff.
11	38	- This is also automagically called when using `pauvre marginplot`

23	50	genomes with the fewest crossings-over. Input is one `.gff` file
24	51	per circular genome and one directory of gene alignments.
25	52
26		# Requirements
	53
	54	## <a name="installation"></a>Installation
	55
	56	### <a name="reqs"></a>Requirements
27	57
28	58	- You must have the following installed on your system to install this software:
29	59	- python 3.x

32	62	- pandas
33	63	- pillow
34	64
35		# Installation
36
	65	### <a name="install">Install Instructions
37	66	- Instructions to install on your mac or linux system. Not sure on
38	67	Windows! Make sure python 3 is the active environment before
39	68	installing.

43	72	- Or, install with pip
44	73	- `pip3 install pauvre`
45	74
46		# Usage
	75	## <a name="usage"><a/>Usage
47	76
48		## `stats`
	77	### <a name="stats"></a>`stats`
49	78	- generate basic statistics about the fastq file. For example, if I
50	79	want to know the number of bases and reads with AT LEAST a PHRED
51	80	score of 5 and AT LEAST a read length of 500, run the program as below

77	106	et cetera...
78	107	```
79	108
80		## `marginplot`
	109	### <a name="marginplot"></a>`marginplot`
81	110
82		### Basic usage
	111	#### <a name="marginbasic"></a>Basic Usage
83	112	- automatically calls `pauvre stats` for each fastq file
84	113	- Make the default plot showing the 99th percentile of longest reads
85	114	- `pauvre marginplot --fastq miniDSMN15.fastq`

89	118	- `pauvre marginplot --maxlen 4000 --maxqual 25 --lengthbin 50 --fileform pdf png --qualbin 0.5 --fastq miniDSMN15.fastq`
90	119	- ![example1](files/miniDSMN15.png)
91	120
92		### Filter reads and adjust viewing window
	121	#### <a name="marginadjustments"></a>Plot Adjustments
	122
93	123	- Filter out reads with a mean quality less than 5, and a length
94	124	less than 800. Zoom in to plot only mean quality of at least 4 and
95	125	read length at least 500bp.
96	126	- `pauvre marginplot -f miniDSMN15.fastq --filt_minqual 5 --filt_minlen 800 -y --plot_minlen 500 --plot_minqual 4`
97	127	- ![test4](files/test4.png)
98	128
99		### Specialized Options
	129	#### <a name="marginspecialized"></a>Specialized Options
100	130
101	131	- Plot ONT 1D data with a large tail
102	132	- `pauvre marginplot --maxlen 100000 --maxqual 15 --lengthbin 500 <myfile>.fastq`
103	133	- Get more resolution on lengths
104	134	- `pauvre marginplot --maxlen 100000 --lengthbin 5 <myfile>.fastq`
105	135
106		### Transparency
107
108	136	- Turn off transparency if you just want a white background
109	137	- `pauvre marginplot --transparent False <myfile>.fastq`
110	138	- Note: transparency is the default behavior
111	139	- ![transparency](files/transparency.001.jpeg)
112	140
113		# Contributors
	141	## <a name="contributors"></a>Contributors
114	142
115	143	@conchoecia (Darrin Schultz)
116	144	@mebbert (Mark Ebbert)

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pauvre/custommargin.py less more

29	29	import os.path as opath
30	30	from sys import stderr
31	31	from pauvre.functions import print_images
	32	from pauvre.marginplot import generate_panel
32	33	from pauvre.stats import stats
33	34	import pauvre.rcparams as rc
34	35	import sys

36	37
37	38	# logging
38	39	logger = logging.getLogger('pauvre')
39
40
41		def generate_panel(panel_left, panel_bottom, panel_width, panel_height,
42		axis_tick_param='both', which_tick_param='both',
43		bottom_tick_param='on', label_bottom_tick_param='on',
44		left_tick_param='on', label_left_tick_param='on',
45		right_tick_param='off', label_right_tick_param='off',
46		top_tick_param='off', label_top_tick_param='off'):
47		"""
48		Setting default panel tick parameters. Some of these are the defaults
49		for matplotlib anyway, but specifying them for readability. Here are
50		options and defaults for the parameters used below:
51
52		axis : {'x', 'y', 'both'}; which axis to modify; default = 'both'
53		which : {'major', 'minor', 'both'}; which ticks to modify;
54		default = 'major'
55		bottom, top, left, right : bool or {'on', 'off'}; ticks on or off;
56		labelbottom, labeltop, labelleft, labelright : bool or {'on', 'off'}
57		"""
58
59		# create the panel
60		panel_rectangle = [panel_left, panel_bottom, panel_width, panel_height]
61		panel = plt.axes(panel_rectangle)
62
63		# Set tick parameters
64		panel.tick_params(axis=axis_tick_param,
65		which=which_tick_param,
66		bottom=bottom_tick_param,
67		labelbottom=label_bottom_tick_param,
68		left=left_tick_param,
69		labelleft=label_left_tick_param,
70		right=right_tick_param,
71		labelright=label_right_tick_param,
72		top=top_tick_param,
73		labeltop=label_top_tick_param)
74
75		return panel
76
77	40
78	41	def _generate_histogram_bin_patches(panel, bins, bin_values, horizontal=True):
79	42	"""This helper method generates the histogram that is added to the panel.

270	233	print(" - Setting panel options.", file = sys.stderr)
271	234	if kwargs["Y_AXES"]:
272	235	y_bottom_spine = True
273		y_bottom_tick = 'on'
274		y_bottom_label = 'on'
	236	y_bottom_tick = True
	237	y_bottom_label = True
275	238	x_left_spine = True
276		x_left_tick = 'on'
277		x_left_label = 'on'
	239	x_left_tick = True
	240	x_left_label = True
278	241	x_y_label = 'Count'
279	242	else:
280	243	y_bottom_spine = False
281		y_bottom_tick = 'off'
282		y_bottom_label = 'off'
	244	y_bottom_tick = False
	245	y_bottom_label = False
283	246	x_left_spine = False
284		x_left_tick = 'off'
285		x_left_label = 'off'
	247	x_left_tick = False
	248	x_left_label = False
286	249	x_y_label = None
287	250
288	251	panels = []

335	298	legend_panel_height = heat_map_panel_height / fig_height
336	299	legend_panel = generate_panel(legend_panel_left, legend_panel_bottom,
337	300	legend_panel_width, legend_panel_height,
338		bottom_tick_param='off',
339		label_bottom_tick_param='off',
340		left_tick_param='off',
341		label_left_tick_param='off',
342		right_tick_param='on',
343		label_right_tick_param='on')
	301	bottom_tick_param=False,
	302	label_bottom_tick_param=False,
	303	left_tick_param=False,
	304	label_left_tick_param=False,
	305	right_tick_param=True,
	306	label_right_tick_param=True)
344	307	panels.append(legend_panel)
345	308
346	309	#

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pauvre/version.py less more

0	0	# -- coding: utf-8 --
1	1
2		__version__ = "0.2.1"
	2	__version__ = "0.2.2"
3	3

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pauvre.egg-info/PKG-INFO less more

0	0	Metadata-Version: 1.2
1	1	Name: pauvre
2		Version: 0.2.1
	2	Version: 0.2.2
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