[med-svn] [Git][med-team/python-pauvre][upstream] New upstream version 0.2.2
Andreas Tille
gitlab at salsa.debian.org
Thu Jun 11 21:41:24 BST 2020
Andreas Tille pushed to branch upstream at Debian Med / python-pauvre
Commits:
f59ed2eb by Andreas Tille at 2020-06-11T22:36:38+02:00
New upstream version 0.2.2
- - - - -
5 changed files:
- PKG-INFO
- README.md
- pauvre.egg-info/PKG-INFO
- pauvre/custommargin.py
- pauvre/version.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.2
Name: pauvre
-Version: 0.2.1
+Version: 0.2.2
Summary: Tools for plotting Oxford Nanopore and other long-read data.
Home-page: https://github.com/conchoecia/pauvre
Author: Darrin Schultz
=====================================
README.md
=====================================
@@ -1,12 +1,39 @@
[](https://travis-ci.org/conchoecia/pauvre) [](https://zenodo.org/badge/latestdoi/112774670)
+## <a name="started"></a>Getting Started
-## pauvre: a plotting package designed for nanopore and PacBio long reads
+```
+pauvre custommargin -i custom.tsv --ycol length --xcol qual # Custom tsv input
+```
+
+## Table of Contents
+
+- [Getting Started](#started)
+- [Users' Guide](#uguide)
+- [Installation](#installation)
+ - [Requirements](#reqs)
+ - [Install Instructions](#install)
+- [Usage](#usage)
+ - [pauvre stats](#stats)
+ - [pauvre marginplot](#marginplot)
+ - [Basic Usage](#marginbasic)
+ - [Plot Adjustments](#marginadjustments)
+ - [Specialized Options](#marginspecialized)
+- [Contributors](#contributors)
+
+## <a name="uguide"></a>Users' Guide
+
+Pauvre is a plotting package originally designed to help QC the length and
+quality distribution of Oxford Nanopore or PacBio reads. The main outputs
+are marginplots. Now, `pauvre` also hosts other additional data plotting
+scripts.
-This package currently hosts four scripts for plotting and/or printing stats.
+This package currently hosts five scripts for plotting and/or printing stats.
- `pauvre marginplot`
- takes a fastq file as input and outputs a marginal histogram with a heatmap.
+- `pauvre custommargin`
+ - takes a tsv as input and outputs a marginal histogram with custom columns of your choice.
- `pauvre stats`
- 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.
- This is also automagically called when using `pauvre marginplot`
@@ -24,7 +51,10 @@ This package currently hosts four scripts for plotting and/or printing stats.
genomes with the fewest crossings-over. Input is one `.gff` file
per circular genome and one directory of gene alignments.
-# Requirements
+
+## <a name="installation"></a>Installation
+
+### <a name="reqs"></a>Requirements
- You must have the following installed on your system to install this software:
- python 3.x
@@ -33,8 +63,7 @@ This package currently hosts four scripts for plotting and/or printing stats.
- pandas
- pillow
-# Installation
-
+### <a name="install">Install Instructions
- Instructions to install on your mac or linux system. Not sure on
Windows! Make sure *python 3* is the active environment before
installing.
@@ -44,9 +73,9 @@ This package currently hosts four scripts for plotting and/or printing stats.
- Or, install with pip
- `pip3 install pauvre`
-# Usage
+## <a name="usage"><a/>Usage
-## `stats`
+### <a name="stats"></a>`stats`
- generate basic statistics about the fastq file. For example, if I
want to know the number of bases and reads with AT LEAST a PHRED
score of 5 and AT LEAST a read length of 500, run the program as below
@@ -78,9 +107,9 @@ minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30
et cetera...
```
-## `marginplot`
+### <a name="marginplot"></a>`marginplot`
-### Basic usage
+#### <a name="marginbasic"></a>Basic Usage
- automatically calls `pauvre stats` for each fastq file
- Make the default plot showing the 99th percentile of longest reads
- `pauvre marginplot --fastq miniDSMN15.fastq`
@@ -90,28 +119,27 @@ minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30
- `pauvre marginplot --maxlen 4000 --maxqual 25 --lengthbin 50 --fileform pdf png --qualbin 0.5 --fastq miniDSMN15.fastq`
- 
-### Filter reads and adjust viewing window
+#### <a name="marginadjustments"></a>Plot Adjustments
+
- Filter out reads with a mean quality less than 5, and a length
less than 800. Zoom in to plot only mean quality of at least 4 and
read length at least 500bp.
- `pauvre marginplot -f miniDSMN15.fastq --filt_minqual 5 --filt_minlen 800 -y --plot_minlen 500 --plot_minqual 4`
- 
-### Specialized Options
+#### <a name="marginspecialized"></a>Specialized Options
- Plot ONT 1D data with a large tail
- `pauvre marginplot --maxlen 100000 --maxqual 15 --lengthbin 500 <myfile>.fastq`
- Get more resolution on lengths
- `pauvre marginplot --maxlen 100000 --lengthbin 5 <myfile>.fastq`
-### Transparency
-
- Turn off transparency if you just want a white background
- `pauvre marginplot --transparent False <myfile>.fastq`
- Note: transparency is the default behavior
- 
-# Contributors
+## <a name="contributors"></a>Contributors
@conchoecia (Darrin Schultz)
@mebbert (Mark Ebbert)
=====================================
pauvre.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.2
Name: pauvre
-Version: 0.2.1
+Version: 0.2.2
Summary: Tools for plotting Oxford Nanopore and other long-read data.
Home-page: https://github.com/conchoecia/pauvre
Author: Darrin Schultz
=====================================
pauvre/custommargin.py
=====================================
@@ -30,6 +30,7 @@ import pandas as pd
import os.path as opath
from sys import stderr
from pauvre.functions import print_images
+from pauvre.marginplot import generate_panel
from pauvre.stats import stats
import pauvre.rcparams as rc
import sys
@@ -38,44 +39,6 @@ import logging
# logging
logger = logging.getLogger('pauvre')
-
-def generate_panel(panel_left, panel_bottom, panel_width, panel_height,
- axis_tick_param='both', which_tick_param='both',
- bottom_tick_param='on', label_bottom_tick_param='on',
- left_tick_param='on', label_left_tick_param='on',
- right_tick_param='off', label_right_tick_param='off',
- top_tick_param='off', label_top_tick_param='off'):
- """
- Setting default panel tick parameters. Some of these are the defaults
- for matplotlib anyway, but specifying them for readability. Here are
- options and defaults for the parameters used below:
-
- axis : {'x', 'y', 'both'}; which axis to modify; default = 'both'
- which : {'major', 'minor', 'both'}; which ticks to modify;
- default = 'major'
- bottom, top, left, right : bool or {'on', 'off'}; ticks on or off;
- labelbottom, labeltop, labelleft, labelright : bool or {'on', 'off'}
- """
-
- # create the panel
- panel_rectangle = [panel_left, panel_bottom, panel_width, panel_height]
- panel = plt.axes(panel_rectangle)
-
- # Set tick parameters
- panel.tick_params(axis=axis_tick_param,
- which=which_tick_param,
- bottom=bottom_tick_param,
- labelbottom=label_bottom_tick_param,
- left=left_tick_param,
- labelleft=label_left_tick_param,
- right=right_tick_param,
- labelright=label_right_tick_param,
- top=top_tick_param,
- labeltop=label_top_tick_param)
-
- return panel
-
-
def _generate_histogram_bin_patches(panel, bins, bin_values, horizontal=True):
"""This helper method generates the histogram that is added to the panel.
@@ -271,19 +234,19 @@ def custommargin(df, **kwargs):
print(" - Setting panel options.", file = sys.stderr)
if kwargs["Y_AXES"]:
y_bottom_spine = True
- y_bottom_tick = 'on'
- y_bottom_label = 'on'
+ y_bottom_tick = True
+ y_bottom_label = True
x_left_spine = True
- x_left_tick = 'on'
- x_left_label = 'on'
+ x_left_tick = True
+ x_left_label = True
x_y_label = 'Count'
else:
y_bottom_spine = False
- y_bottom_tick = 'off'
- y_bottom_label = 'off'
+ y_bottom_tick = False
+ y_bottom_label = False
x_left_spine = False
- x_left_tick = 'off'
- x_left_label = 'off'
+ x_left_tick = False
+ x_left_label = False
x_y_label = None
panels = []
@@ -336,12 +299,12 @@ def custommargin(df, **kwargs):
legend_panel_height = heat_map_panel_height / fig_height
legend_panel = generate_panel(legend_panel_left, legend_panel_bottom,
legend_panel_width, legend_panel_height,
- bottom_tick_param='off',
- label_bottom_tick_param='off',
- left_tick_param='off',
- label_left_tick_param='off',
- right_tick_param='on',
- label_right_tick_param='on')
+ bottom_tick_param=False,
+ label_bottom_tick_param=False,
+ left_tick_param=False,
+ label_left_tick_param=False,
+ right_tick_param=True,
+ label_right_tick_param=True)
panels.append(legend_panel)
#
=====================================
pauvre/version.py
=====================================
@@ -1,4 +1,4 @@
# -*- coding: utf-8 -*-
-__version__ = "0.2.1"
+__version__ = "0.2.2"
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/commit/f59ed2eb09a7ba2ccf27880a3470a7c275c79742
--
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/commit/f59ed2eb09a7ba2ccf27880a3470a7c275c79742
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