[med-svn] [Git][med-team/python-pauvre][master] 7 commits: New upstream version 0.2.2
Andreas Tille
gitlab at salsa.debian.org
Thu Jun 11 21:41:21 BST 2020
Andreas Tille pushed to branch master at Debian Med / python-pauvre
Commits:
f59ed2eb by Andreas Tille at 2020-06-11T22:36:38+02:00
New upstream version 0.2.2
- - - - -
6d382904 by Andreas Tille at 2020-06-11T22:36:38+02:00
routine-update: New upstream version
- - - - -
3423d14e by Andreas Tille at 2020-06-11T22:36:39+02:00
Update upstream source from tag 'upstream/0.2.2'
Update to upstream version '0.2.2'
with Debian dir 32779528b613632d498a9901a1ab8d0fe1df32a2
- - - - -
f7d87624 by Andreas Tille at 2020-06-11T22:36:39+02:00
routine-update: debhelper-compat 13
- - - - -
dec5390f by Andreas Tille at 2020-06-11T22:36:43+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2a5f781d by Andreas Tille at 2020-06-11T22:36:46+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
7162608d by Andreas Tille at 2020-06-11T22:40:21+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- PKG-INFO
- README.md
- debian/changelog
- debian/control
- + debian/upstream/metadata
- 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)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-pauvre (0.2.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Jun 2020 22:36:46 +0200
+
python-pauvre (0.2.1-1) unstable; urgency=medium
* Initial release (Closes: #958951)
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-setuptools,
@@ -18,6 +18,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre
Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git
Homepage: https://github.com/conchoecia/pauvre
+Rules-Requires-Root: no
Package: python3-pauvre
Architecture: all
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,3 @@
+---
+Bug-Database: https://github.com/conchoecia/pauvre/issues
+Bug-Submit: https://github.com/conchoecia/pauvre/issues/new
=====================================
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/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227
--
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227
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