New Upstream Snapshot - python-nanomath

Ready changes

Summary

Merged new upstream version: 1.2.1+git20210604.1.79b7f85+ds (was: 1.2.1+ds).

Resulting package

Built on 2023-01-20T06:02 (took 13m56s)

The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:

apt install -t fresh-snapshots python3-nanomath

Diff

diff --git a/PKG-INFO b/PKG-INFO
index 3aaf2c1..a015165 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,4 +1,4 @@
-Metadata-Version: 1.2
+Metadata-Version: 2.1
 Name: nanomath
 Version: 1.2.1
 Summary: A few simple math function for other Oxford Nanopore processing scripts
@@ -6,47 +6,7 @@ Home-page: https://github.com/wdecoster/nanomath
 Author: Wouter De Coster
 Author-email: decosterwouter@gmail.com
 License: GPLv3
-Description: # nanomath
-        This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
-        
-        [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
-        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
-        [![install with Debian](https://www.debian.org/logos/button-mini.png)](https://tracker.debian.org/pkg/python-nanomath)
-        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
-        [![Code Health](https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanomath/master)
-        
-        
-        ## FUNCTIONS
-        * Calculate read N50 from a set of lengths `get_N50(readlenghts)`  
-        * Remove extreme length outliers from a dataset `remove_length_outliers(dataframe, columname)`  
-        * Calculate the average Phred quality of a read `ave_qual(qualscores)`  
-        * Write out the statistics report after calling readstats function `write_stats(dataframe, outputname)`  
-        * Compute a number of statistics, return a dictionary `calc_read_stats(dataframe)`  
-        
-        
-        ## INSTALLATION
-        ```bash
-        pip install nanomath
-        ```
-        or  
-        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
-        ```
-        conda install -c bioconda nanomath
-        ```
-        
-        ## STATUS 
-        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
-        
-        
-        ## CONTRIBUTORS
-        [@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
-        
-        
-        ## CITATION
-        If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
-        
 Keywords: nanopore sequencing plotting quality control
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
@@ -56,3 +16,43 @@ Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
 Classifier: Programming Language :: Python :: 3.5
 Requires-Python: >=3
+License-File: LICENSE
+
+# nanomath
+This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
+
+[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
+[![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
+[![install with Debian](https://www.debian.org/logos/button-mini.png)](https://tracker.debian.org/pkg/python-nanomath)
+[![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
+[![Code Health](https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanomath/master)
+
+
+## FUNCTIONS
+* Calculate read N50 from a set of lengths `get_N50(readlenghts)`  
+* Remove extreme length outliers from a dataset `remove_length_outliers(dataframe, columname)`  
+* Calculate the average Phred quality of a read `ave_qual(qualscores)`  
+* Write out the statistics report after calling readstats function `write_stats(dataframe, outputname)`  
+* Compute a number of statistics, return a dictionary `calc_read_stats(dataframe)`  
+
+
+## INSTALLATION
+```bash
+pip install nanomath
+```
+or  
+[![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
+```
+conda install -c bioconda nanomath
+```
+
+## STATUS 
+[![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
+
+
+## CONTRIBUTORS
+[@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
+
+
+## CITATION
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
diff --git a/README.rst b/README.rst
deleted file mode 100644
index 731fb2c..0000000
--- a/README.rst
+++ /dev/null
@@ -1,63 +0,0 @@
-nanomath
-========
-
-This module provides a few simple math and statistics functions for
-other scripts processing Oxford Nanopore sequencing data
-
-|Twitter URL| |install with conda| |install with Debian| |Build Status|
-|Code Health|
-
-FUNCTIONS
----------
-
--  Calculate read N50 from a set of lengths ``get_N50(readlenghts)``
--  Remove extreme length outliers from a dataset
-   ``remove_length_outliers(dataframe, columname)``
--  Calculate the average Phred quality of a read
-   ``ave_qual(qualscores)``
--  Write out the statistics report after calling readstats function
-   ``write_stats(dataframe, outputname)``
--  Compute a number of statistics, return a dictionary
-   ``calc_read_stats(dataframe)``
-
-INSTALLATION
-------------
-
-.. code:: bash
-
-   pip install nanomath
-
-| or
-| |install with conda|
-
-::
-
-   conda install -c bioconda nanomath
-
-STATUS
-------
-
-|Build Status|
-
-CONTRIBUTORS
-------------
-
-[@alexomics](https://github.com/alexomics) for fixing the indentation of
-the printed stats
-
-CITATION
---------
-
-If you use this tool, please consider citing our
-`publication <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
-
-.. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
-   :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
-   :target: https://landscape.io/github/wdecoster/nanomath/master
diff --git a/debian/changelog b/debian/changelog
index 3389544..a64cb0a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-nanomath (1.2.1+git20210604.1.79b7f85+ds-1) UNRELEASED; urgency=low
+
+  * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Fri, 20 Jan 2023 05:50:47 -0000
+
 python-nanomath (1.2.1+ds-1) unstable; urgency=medium
 
   * New upstream version 1.2.1+ds
diff --git a/nanomath.egg-info/PKG-INFO b/nanomath.egg-info/PKG-INFO
index 3aaf2c1..a015165 100644
--- a/nanomath.egg-info/PKG-INFO
+++ b/nanomath.egg-info/PKG-INFO
@@ -1,4 +1,4 @@
-Metadata-Version: 1.2
+Metadata-Version: 2.1
 Name: nanomath
 Version: 1.2.1
 Summary: A few simple math function for other Oxford Nanopore processing scripts
@@ -6,47 +6,7 @@ Home-page: https://github.com/wdecoster/nanomath
 Author: Wouter De Coster
 Author-email: decosterwouter@gmail.com
 License: GPLv3
-Description: # nanomath
-        This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
-        
-        [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
-        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
-        [![install with Debian](https://www.debian.org/logos/button-mini.png)](https://tracker.debian.org/pkg/python-nanomath)
-        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
-        [![Code Health](https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanomath/master)
-        
-        
-        ## FUNCTIONS
-        * Calculate read N50 from a set of lengths `get_N50(readlenghts)`  
-        * Remove extreme length outliers from a dataset `remove_length_outliers(dataframe, columname)`  
-        * Calculate the average Phred quality of a read `ave_qual(qualscores)`  
-        * Write out the statistics report after calling readstats function `write_stats(dataframe, outputname)`  
-        * Compute a number of statistics, return a dictionary `calc_read_stats(dataframe)`  
-        
-        
-        ## INSTALLATION
-        ```bash
-        pip install nanomath
-        ```
-        or  
-        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
-        ```
-        conda install -c bioconda nanomath
-        ```
-        
-        ## STATUS 
-        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
-        
-        
-        ## CONTRIBUTORS
-        [@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
-        
-        
-        ## CITATION
-        If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
-        
 Keywords: nanopore sequencing plotting quality control
-Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
@@ -56,3 +16,43 @@ Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
 Classifier: Programming Language :: Python :: 3.5
 Requires-Python: >=3
+License-File: LICENSE
+
+# nanomath
+This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
+
+[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
+[![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
+[![install with Debian](https://www.debian.org/logos/button-mini.png)](https://tracker.debian.org/pkg/python-nanomath)
+[![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
+[![Code Health](https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanomath/master)
+
+
+## FUNCTIONS
+* Calculate read N50 from a set of lengths `get_N50(readlenghts)`  
+* Remove extreme length outliers from a dataset `remove_length_outliers(dataframe, columname)`  
+* Calculate the average Phred quality of a read `ave_qual(qualscores)`  
+* Write out the statistics report after calling readstats function `write_stats(dataframe, outputname)`  
+* Compute a number of statistics, return a dictionary `calc_read_stats(dataframe)`  
+
+
+## INSTALLATION
+```bash
+pip install nanomath
+```
+or  
+[![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
+```
+conda install -c bioconda nanomath
+```
+
+## STATUS 
+[![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
+
+
+## CONTRIBUTORS
+[@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
+
+
+## CITATION
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
diff --git a/nanomath/nanomath.py b/nanomath/nanomath.py
index 5d260fc..f02fe90 100644
--- a/nanomath/nanomath.py
+++ b/nanomath/nanomath.py
@@ -27,6 +27,11 @@ from math import log
 
 class Stats(object):
     def __init__(self, df):
+        if len(df) < 5:
+            sys.stderr.write("\n\nWARNING: less than 5 reads in the dataset!\n")
+            sys.stderr.write("WARNING: some stats might be unexpected or missing\n")
+            sys.stderr.write("WARNING: or a crash might happen, who knows\n")
+            sys.stderr.write("WARNING: this code is not intended for such small datasets\n\n\n")
         self.number_of_reads = len(df)
         self.number_of_bases = np.sum(df["lengths"])
         self._with_readIDs = "readIDs" in df

Debdiff

File lists identical (after any substitutions)

No differences were encountered in the control files

More details

Full run details