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]))] -@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 You're receiving this email because of your account on salsa.debian.org.
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