[med-svn] [Git][med-team/python-nanomath][upstream] New upstream version 1.2.0+ds
Nilesh Patra
gitlab at salsa.debian.org
Tue Dec 22 18:01:21 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / python-nanomath
Commits:
55a3a273 by Nilesh Patra at 2020-12-22T23:25:34+05:30
New upstream version 1.2.0+ds
- - - - -
6 changed files:
- PKG-INFO
- README.md
- README.rst
- nanomath.egg-info/PKG-INFO
- nanomath/nanomath.py
- nanomath/version.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.2
Name: nanomath
-Version: 1.0.1
+Version: 1.2.0
Summary: A few simple math function for other Oxford Nanopore processing scripts
Home-page: https://github.com/wdecoster/nanomath
Author: Wouter De Coster
@@ -11,6 +11,7 @@ Description: # nanomath
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanomath)
+ [](https://tracker.debian.org/pkg/python-nanomath)
[](https://travis-ci.org/wdecoster/nanomath)
[](https://landscape.io/github/wdecoster/nanomath/master)
@@ -33,7 +34,7 @@ Description: # nanomath
conda install -c bioconda nanomath
```
- ## STATUS
+ ## STATUS
[](https://travis-ci.org/wdecoster/nanomath)
=====================================
README.md
=====================================
@@ -3,6 +3,7 @@ This module provides a few simple math and statistics functions for other script
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanomath)
+[](https://tracker.debian.org/pkg/python-nanomath)
[](https://travis-ci.org/wdecoster/nanomath)
[](https://landscape.io/github/wdecoster/nanomath/master)
@@ -25,7 +26,7 @@ or
conda install -c bioconda nanomath
```
-## STATUS
+## STATUS
[](https://travis-ci.org/wdecoster/nanomath)
=====================================
README.rst
=====================================
@@ -4,7 +4,8 @@ nanomath
This module provides a few simple math and statistics functions for
other scripts processing Oxford Nanopore sequencing data
-|Twitter URL| |install with conda| |Build Status| |Code Health|
+|Twitter URL| |install with conda| |install with Debian| |Build Status|
+|Code Health|
FUNCTIONS
---------
@@ -54,6 +55,8 @@ If you use this tool, please consider citing our
:target: https://twitter.com/wouter_decoster
.. |install with conda| image:: https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg
:target: https://anaconda.org/bioconda/nanomath
+.. |install with Debian| image:: https://www.debian.org/logos/button-mini.png
+ :target: https://tracker.debian.org/pkg/python-nanomath
.. |Build Status| image:: https://travis-ci.org/wdecoster/nanomath.svg?branch=master
:target: https://travis-ci.org/wdecoster/nanomath
.. |Code Health| image:: https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat
=====================================
nanomath.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.2
Name: nanomath
-Version: 1.0.1
+Version: 1.2.0
Summary: A few simple math function for other Oxford Nanopore processing scripts
Home-page: https://github.com/wdecoster/nanomath
Author: Wouter De Coster
@@ -11,6 +11,7 @@ Description: # nanomath
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanomath)
+ [](https://tracker.debian.org/pkg/python-nanomath)
[](https://travis-ci.org/wdecoster/nanomath)
[](https://landscape.io/github/wdecoster/nanomath/master)
@@ -33,7 +34,7 @@ Description: # nanomath
conda install -c bioconda nanomath
```
- ## STATUS
+ ## STATUS
[](https://travis-ci.org/wdecoster/nanomath)
=====================================
nanomath/nanomath.py
=====================================
@@ -32,8 +32,10 @@ class Stats(object):
self._with_readIDs = "readIDs" in df
if "aligned_lengths" in df:
self.number_of_bases_aligned = np.sum(df["aligned_lengths"])
+ self.fraction_bases_aligned = self.number_of_bases_aligned / self.number_of_bases
self.median_read_length = np.median(df["lengths"])
self.mean_read_length = np.mean(df["lengths"])
+ self.read_length_stdev = np.std(df["lengths"])
self.n50 = get_N50(np.sort(df["lengths"]))
if "percentIdentity" in df:
self.average_identity = np.mean(df["percentIdentity"])
@@ -122,7 +124,6 @@ def remove_length_outliers(df, columnname):
return df[df[columnname] < (np.median(df[columnname]) + 3 * np.std(df[columnname]))]
- at deprecated
def errs_tab(n):
"""Generate list of error rates for qualities less than equal than n."""
return [10**(q / -10) for q in range(n+1)]
@@ -198,8 +199,10 @@ def write_stats_legacy(stats, names, output, datadfs):
"Number of reads": "number_of_reads",
"Total bases": "number_of_bases",
"Total bases aligned": "number_of_bases_aligned",
+ "Fraction of bases aligned": "fraction_bases_aligned",
"Median read length": "median_read_length",
"Mean read length": "mean_read_length",
+ "STDEV read length": "read_length_stdev",
"Read length N50": "n50",
"Average percent identity": "average_identity",
"Median percent identity": "median_identity",
=====================================
nanomath/version.py
=====================================
@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.2.0"
View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/commit/55a3a27328ad97ea6148b62712340ffe13c219fb
--
View it on GitLab: https://salsa.debian.org/med-team/python-nanomath/-/commit/55a3a27328ad97ea6148b62712340ffe13c219fb
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