pupmapper 0.0.5__tar.gz

pupmapper-0.0.5/.gitignore

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pupmapper-0.0.5/LICENSE

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+MIT License
+
+Copyright (c) 2024 Maximillian Marin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pupmapper-0.0.5/PKG-INFO

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+Metadata-Version: 2.1
+Name: pupmapper
+Version: 0.0.5
+Summary: Tool & python package for calculating genome wide pileup mappability
+Project-URL: Homepage, https://github.com/maxgmarin/pupmapper
+Author-email: Maximillian Marin <maximilliangmarin@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.8
+Requires-Dist: bioframe>=0.7.2
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pybigtools==0.2.1
+Requires-Dist: tqdm
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+<img width="500" src="https://github.com/maxgmarin/pupmapper/raw/main/Images/pupmapper.logo.png" alt="pupmapper logo">
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+![Static Badge](https://img.shields.io/badge/language-Python_3-blue)
+<!---[![Build Status]()]()
+[![github release version]()]()
+[![DOI]()]()
+--->
+
+Pupmapper: A **P**ile**up** **Map**pability Calculato**r** 
+
+<!---
+> TBD Reference
+--->
+
+[TOC]: #
+## Table of Contents
+- [Motivation](#motivation)
+- [Installation](#installation)
+  - [Install locally](#install-locally)
+  - [`pip`](#pip)
+- [Basic usage](#basic-usage)
+  - [test data set](#analyzing-included-test-data-set)
+- [Full usage](#full-usage)
+
+
+## Motivation
+The Pileup Mappability metric can be used to quickly identify regions which may be more difficult to perform variant calling with short-read WGS data. `pupmapper` was created to allow users to quickly convert k-mer mappability scores to pileup mappability. 
+
+The first step of the `pupmapper` pipeline is to calculate k-mer uniquness scores using the [Genmap](https://github.com/cpockrandt/genmap) software. Then pupmapper will summarize the pileup mappability of each genomic position using the k-mer uniqueness of all overlapping k-mers.
+
+
+### How is pileup mappability calculated from individual k-mer uniqueness/mappability scores?
+
+<img width="500" src="https://github.com/maxgmarin/pupmapper/raw/main/Images/Derrien2012.PmapFig.png" alt="PmapFig">
+The Pileup mappability of a position is specifically calculated as the mean k-mer mappability of all k-mers overlapping a given position. <br>
+
+A pileup mappability score of 1 indicates that all k-mers overlapping with a position are unique within the genome (using the user defined parameters of uniqueness).
+
+**Pileup mappability is useful because it gives a sense of uniquemess of all possible reads (of defined length) that could align to a given position.**
+
+
+### Useful reading for k-mer mappability and pileup mappability:
+
+> Derrien, T, (2012). Fast Computation and Applications of Genome Mappability. PLOS ONE 7(1): e30377. [https://doi.org/10.1371/journal.pone.0030377](https://doi.org/10.1371/journal.pone.0030377)
+
+> Pockrandt C, (2020) GenMap: ultra-fast computation of genome mappability, Bioinformatics, Volume 36, Issue 12, June 2020, Pages 3687–3692, [https://doi.org/10.1093/bioinformatics/btaa222](https://doi.org/10.1093/bioinformatics/btaa222)
+
+> Lee H, Schatz MC. (2012). Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score, Bioinformatics, Volume 28, Issue 16, August 2012, Pages 2097–2105, [https://doi.org/10.1093/bioinformatics/bts330](https://doi.org/10.1093/bioinformatics/bts330)
+
+## Installation
+### Install locally
+`pupmapper` can be installed by cloning this repository and installing with `pip`.
+
+```
+git clone git@github.com:maxgmarin/pupmapper.git
+
+cd pupmapper
+
+pip install . 
+```
+
+### `pip`
+>🚧 Check back soon 🚧
+
+### `conda`
+>🚧 Check back soon 🚧
+
+
+## Basic usage
+
+
+#### 1) `run_all` - Run the full pipeline starting with an input genome
+
+```
+pupmapper run_all -i Input.Genome.fasta -o output_directory/ -k 50 -e 1
+```
+The above command will first use genmap to calculate k-mer mappability scores for the input genome and then calculate pileup mappability scores.
+
+Arguments:
+
+`-i, --in_genome_fa`: Input genome FASTA file. <br>
+`-o, --outdir`: Directory for output files. <br>
+`-k, --kmer_len`: K-mer length (e.g., 50 bp). <br>
+`-e, --errors`: Number of allowed mismatches in k-mer mapping. <br>
+`-g, --gff`: (Optional) Input genome annotations in GFF format. <br>
+`--save-numpy`: (Optional) Save results as compressed numpy arrays. <br>
+
+
+### Analyzing included test sequence
+
+If you wish to run an `pupmapper` on a small test sequence (15 bp), you can run the following commands:
+```
+cd tests/data/Genmap_Ex1/
+
+pupmapper run_all -i Ex1.genome.fasta -o Ex1_OutputDir -k 4 -e 0
+```
+This command will analyze the pileup mappability of the test sequence with a k-mer size of 4 bp and a max mismatch of 0 (K=4,E=0).
+
+
+## Full usage
+```
+pupmapper run_all --help
+usage: pupmapper run_all [-h] -i IN_GENOME_FA -o OUTDIR -k KMER_LEN -e ERRORS [-g GFF] [--save-numpy]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i IN_GENOME_FA, --in_genome_fa IN_GENOME_FA
+                        Input genome fasta file (.fasta)
+  -o OUTDIR, --outdir OUTDIR
+                        Directory for all outputs of k-mer and pileup mappability processing.
+  -k KMER_LEN, --kmer_len KMER_LEN
+                        k-mer length (bp) used to generate the k-mer mappability values
+  -e ERRORS, --errors ERRORS
+                        Number of errors (mismatches) allowed in Genmap's k-mer mappability calculation
+  -g GFF, --gff GFF     GFF formatted genome annotations for input genome (.gff) (Optional)
+  --save-numpy          If enabled, all pileup mappability scores will be output as compressed numpy arrays (.npz).
+```
+
+
+
+
+
+

pupmapper-0.0.5/README.md

@@ -0,0 +1,124 @@
+<img width="500" src="https://github.com/maxgmarin/pupmapper/raw/main/Images/pupmapper.logo.png" alt="pupmapper logo">
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+![Static Badge](https://img.shields.io/badge/language-Python_3-blue)
+<!---[![Build Status]()]()
+[![github release version]()]()
+[![DOI]()]()
+--->
+
+Pupmapper: A **P**ile**up** **Map**pability Calculato**r** 
+
+<!---
+> TBD Reference
+--->
+
+[TOC]: #
+## Table of Contents
+- [Motivation](#motivation)
+- [Installation](#installation)
+  - [Install locally](#install-locally)
+  - [`pip`](#pip)
+- [Basic usage](#basic-usage)
+  - [test data set](#analyzing-included-test-data-set)
+- [Full usage](#full-usage)
+
+
+## Motivation
+The Pileup Mappability metric can be used to quickly identify regions which may be more difficult to perform variant calling with short-read WGS data. `pupmapper` was created to allow users to quickly convert k-mer mappability scores to pileup mappability. 
+
+The first step of the `pupmapper` pipeline is to calculate k-mer uniquness scores using the [Genmap](https://github.com/cpockrandt/genmap) software. Then pupmapper will summarize the pileup mappability of each genomic position using the k-mer uniqueness of all overlapping k-mers.
+
+
+### How is pileup mappability calculated from individual k-mer uniqueness/mappability scores?
+
+<img width="500" src="https://github.com/maxgmarin/pupmapper/raw/main/Images/Derrien2012.PmapFig.png" alt="PmapFig">
+The Pileup mappability of a position is specifically calculated as the mean k-mer mappability of all k-mers overlapping a given position. <br>
+
+A pileup mappability score of 1 indicates that all k-mers overlapping with a position are unique within the genome (using the user defined parameters of uniqueness).
+
+**Pileup mappability is useful because it gives a sense of uniquemess of all possible reads (of defined length) that could align to a given position.**
+
+
+### Useful reading for k-mer mappability and pileup mappability:
+
+> Derrien, T, (2012). Fast Computation and Applications of Genome Mappability. PLOS ONE 7(1): e30377. [https://doi.org/10.1371/journal.pone.0030377](https://doi.org/10.1371/journal.pone.0030377)
+
+> Pockrandt C, (2020) GenMap: ultra-fast computation of genome mappability, Bioinformatics, Volume 36, Issue 12, June 2020, Pages 3687–3692, [https://doi.org/10.1093/bioinformatics/btaa222](https://doi.org/10.1093/bioinformatics/btaa222)
+
+> Lee H, Schatz MC. (2012). Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score, Bioinformatics, Volume 28, Issue 16, August 2012, Pages 2097–2105, [https://doi.org/10.1093/bioinformatics/bts330](https://doi.org/10.1093/bioinformatics/bts330)
+
+## Installation
+### Install locally
+`pupmapper` can be installed by cloning this repository and installing with `pip`.
+
+```
+git clone git@github.com:maxgmarin/pupmapper.git
+
+cd pupmapper
+
+pip install . 
+```
+
+### `pip`
+>🚧 Check back soon 🚧
+
+### `conda`
+>🚧 Check back soon 🚧
+
+
+## Basic usage
+
+
+#### 1) `run_all` - Run the full pipeline starting with an input genome
+
+```
+pupmapper run_all -i Input.Genome.fasta -o output_directory/ -k 50 -e 1
+```
+The above command will first use genmap to calculate k-mer mappability scores for the input genome and then calculate pileup mappability scores.
+
+Arguments:
+
+`-i, --in_genome_fa`: Input genome FASTA file. <br>
+`-o, --outdir`: Directory for output files. <br>
+`-k, --kmer_len`: K-mer length (e.g., 50 bp). <br>
+`-e, --errors`: Number of allowed mismatches in k-mer mapping. <br>
+`-g, --gff`: (Optional) Input genome annotations in GFF format. <br>
+`--save-numpy`: (Optional) Save results as compressed numpy arrays. <br>
+
+
+### Analyzing included test sequence
+
+If you wish to run an `pupmapper` on a small test sequence (15 bp), you can run the following commands:
+```
+cd tests/data/Genmap_Ex1/
+
+pupmapper run_all -i Ex1.genome.fasta -o Ex1_OutputDir -k 4 -e 0
+```
+This command will analyze the pileup mappability of the test sequence with a k-mer size of 4 bp and a max mismatch of 0 (K=4,E=0).
+
+
+## Full usage
+```
+pupmapper run_all --help
+usage: pupmapper run_all [-h] -i IN_GENOME_FA -o OUTDIR -k KMER_LEN -e ERRORS [-g GFF] [--save-numpy]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i IN_GENOME_FA, --in_genome_fa IN_GENOME_FA
+                        Input genome fasta file (.fasta)
+  -o OUTDIR, --outdir OUTDIR
+                        Directory for all outputs of k-mer and pileup mappability processing.
+  -k KMER_LEN, --kmer_len KMER_LEN
+                        k-mer length (bp) used to generate the k-mer mappability values
+  -e ERRORS, --errors ERRORS
+                        Number of errors (mismatches) allowed in Genmap's k-mer mappability calculation
+  -g GFF, --gff GFF     GFF formatted genome annotations for input genome (.gff) (Optional)
+  --save-numpy          If enabled, all pileup mappability scores will be output as compressed numpy arrays (.npz).
+```
+
+
+
+
+
+

pupmapper-0.0.5/dev/README.md

@@ -0,0 +1,3 @@
+# Dev directory
+
+This directory is meant for code development and Jupyter notebooks related to pupmapper.