From 64eca40acb2b237d1783c7ac12e55b7e31c68b94 Mon Sep 17 00:00:00 2001 From: Steffen Moeller Date: Wed, 10 Jun 2020 02:13:58 +0200 Subject: Import python-pymummer_0.11.0.orig.tar.gz [dgit import orig python-pymummer_0.11.0.orig.tar.gz] --- .gitignore | 54 ++ .travis.yml | 17 + AUTHORS | 2 + CHANGELOG.md | 135 ++++ LICENSE | 679 +++++++++++++++++++++ README.md | 94 +++ install_dependencies.sh | 69 +++ pymummer/__init__.py | 19 + pymummer/alignment.py | 219 +++++++ pymummer/coords_file.py | 47 ++ pymummer/nucmer.py | 147 +++++ pymummer/snp.py | 45 ++ pymummer/snp_file.py | 24 + pymummer/syscall.py | 30 + pymummer/tests/alignment_test.py | 333 ++++++++++ pymummer/tests/coords_file_test.py | 51 ++ .../coords_file_test_convert_to_msp_crunch.coords | 7 + ...ile_test_convert_to_msp_crunch.no_offset.crunch | 3 + .../coords_file_test_convert_to_msp_crunch.qry.fa | 24 + ...ords_file_test_convert_to_msp_crunch.qry.fa.fai | 3 + .../coords_file_test_convert_to_msp_crunch.ref.fa | 27 + ...ords_file_test_convert_to_msp_crunch.ref.fa.fai | 3 + ...e_test_convert_to_msp_crunch.with_offset.crunch | 3 + .../tests/data/coords_file_test_no_header.coords | 3 + .../tests/data/coords_file_test_with_header.coords | 7 + pymummer/tests/data/nucmer_test_out.coords | 1 + pymummer/tests/data/nucmer_test_out.coords.snps | 2 + pymummer/tests/data/nucmer_test_qry.fa | 15 + pymummer/tests/data/nucmer_test_ref.fa | 18 + .../tests/data/nucmer_test_write_script_no_snps.sh | 3 + .../data/nucmer_test_write_script_with_snps.sh | 4 + .../tests/data/snp_file_test_get_all_variants.snps | 8 + pymummer/tests/data/snp_file_test_no_header.snps | 3 + pymummer/tests/data/snp_file_test_with_header.snps | 7 + pymummer/tests/nucmer_test.py | 99 +++ pymummer/tests/snp_file_test.py | 58 ++ pymummer/tests/snp_test.py | 24 + pymummer/tests/syscall_test.py | 16 + pymummer/tests/variant_test.py | 103 ++++ pymummer/variant.py | 85 +++ setup.py | 45 ++ 41 files changed, 2536 insertions(+) create mode 100644 .gitignore create mode 100644 .travis.yml create mode 100644 AUTHORS create mode 100644 CHANGELOG.md create mode 100644 LICENSE create mode 100644 README.md create mode 100644 install_dependencies.sh create mode 100644 pymummer/__init__.py create mode 100644 pymummer/alignment.py create mode 100644 pymummer/coords_file.py create mode 100644 pymummer/nucmer.py create mode 100644 pymummer/snp.py create mode 100644 pymummer/snp_file.py create mode 100644 pymummer/syscall.py create mode 100644 pymummer/tests/alignment_test.py create mode 100644 pymummer/tests/coords_file_test.py create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai create mode 100644 pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch create mode 100644 pymummer/tests/data/coords_file_test_no_header.coords create mode 100644 pymummer/tests/data/coords_file_test_with_header.coords create mode 100644 pymummer/tests/data/nucmer_test_out.coords create mode 100644 pymummer/tests/data/nucmer_test_out.coords.snps create mode 100644 pymummer/tests/data/nucmer_test_qry.fa create mode 100644 pymummer/tests/data/nucmer_test_ref.fa create mode 100644 pymummer/tests/data/nucmer_test_write_script_no_snps.sh create mode 100644 pymummer/tests/data/nucmer_test_write_script_with_snps.sh create mode 100644 pymummer/tests/data/snp_file_test_get_all_variants.snps create mode 100644 pymummer/tests/data/snp_file_test_no_header.snps create mode 100644 pymummer/tests/data/snp_file_test_with_header.snps create mode 100644 pymummer/tests/nucmer_test.py create mode 100644 pymummer/tests/snp_file_test.py create mode 100644 pymummer/tests/snp_test.py create mode 100644 pymummer/tests/syscall_test.py create mode 100644 pymummer/tests/variant_test.py create mode 100644 pymummer/variant.py create mode 100644 setup.py diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..db4561e --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..b33c035 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,17 @@ +language: python +addons: + apt: + packages: + - g++ + - python-dev +cache: + directories: + - "build" + - "$HOME/.cache/pip" +python: + - "3.3" + - "3.4" +sudo: false +install: + - "source ./install_dependencies.sh" +script: "python setup.py test" diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000..dcb15cd --- /dev/null +++ b/AUTHORS @@ -0,0 +1,2 @@ +Martin Hunt (path-help@sanger.ac.uk) +Nishadi De Silva (path-help@sanger.ac.uk) diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..e61cf7d --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,135 @@ +# Change Log + +## [Unreleased](https://github.com/sanger-pathogens/pymummer/tree/HEAD) + +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.3...HEAD) + +**Merged pull requests:** + +- update README [\#29](https://github.com/sanger-pathogens/pymummer/pull/29) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [v0.10.3](https://github.com/sanger-pathogens/pymummer/tree/v0.10.3) (2017-08-21) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.2...v0.10.3) + +**Merged pull requests:** + +- Add diagfactor \(-d\) and maxgap \(-g\) options for nucmer [\#28](https://github.com/sanger-pathogens/pymummer/pull/28) ([Adamtaranto](https://github.com/Adamtaranto)) +- update LICENSE [\#27](https://github.com/sanger-pathogens/pymummer/pull/27) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [v0.10.2](https://github.com/sanger-pathogens/pymummer/tree/v0.10.2) (2017-02-02) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.1...v0.10.2) + +**Closed issues:** + +- MUMmer programs not found in path [\#21](https://github.com/sanger-pathogens/pymummer/issues/21) + +**Merged pull requests:** + +- Ref qry translate vars not in matches [\#26](https://github.com/sanger-pathogens/pymummer/pull/26) ([martinghunt](https://github.com/martinghunt)) + +## [v0.10.1](https://github.com/sanger-pathogens/pymummer/tree/v0.10.1) (2016-11-18) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.0...v0.10.1) + +**Merged pull requests:** + +- Indels bug [\#25](https://github.com/sanger-pathogens/pymummer/pull/25) ([martinghunt](https://github.com/martinghunt)) + +## [v0.10.0](https://github.com/sanger-pathogens/pymummer/tree/v0.10.0) (2016-11-15) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.9.0...v0.10.0) + +**Merged pull requests:** + +- Show snps expose C option [\#24](https://github.com/sanger-pathogens/pymummer/pull/24) ([martinghunt](https://github.com/martinghunt)) + +## [v0.9.0](https://github.com/sanger-pathogens/pymummer/tree/v0.9.0) (2016-10-17) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.8.1...v0.9.0) + +**Merged pull requests:** + +- Expose mincluster [\#23](https://github.com/sanger-pathogens/pymummer/pull/23) ([martinghunt](https://github.com/martinghunt)) + +## [v0.8.1](https://github.com/sanger-pathogens/pymummer/tree/v0.8.1) (2016-08-23) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.8.0...v0.8.1) + +## [v0.8.0](https://github.com/sanger-pathogens/pymummer/tree/v0.8.0) (2016-08-23) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.7.1...v0.8.0) + +**Merged pull requests:** + +- Ref coords from qry coord [\#22](https://github.com/sanger-pathogens/pymummer/pull/22) ([martinghunt](https://github.com/martinghunt)) + +## [v0.7.1](https://github.com/sanger-pathogens/pymummer/tree/v0.7.1) (2016-04-18) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.7.0...v0.7.1) + +**Merged pull requests:** + +- Make \_\_version\_\_ work [\#20](https://github.com/sanger-pathogens/pymummer/pull/20) ([martinghunt](https://github.com/martinghunt)) + +## [v0.7.0](https://github.com/sanger-pathogens/pymummer/tree/v0.7.0) (2016-02-09) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.6.1...v0.7.0) + +**Merged pull requests:** + +- Coords finding in matches [\#19](https://github.com/sanger-pathogens/pymummer/pull/19) ([martinghunt](https://github.com/martinghunt)) + +## [v0.6.1](https://github.com/sanger-pathogens/pymummer/tree/v0.6.1) (2015-10-19) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.6.0...v0.6.1) + +**Merged pull requests:** + +- Remove numpy dependency [\#18](https://github.com/sanger-pathogens/pymummer/pull/18) ([martinghunt](https://github.com/martinghunt)) + +## [v0.6.0](https://github.com/sanger-pathogens/pymummer/tree/v0.6.0) (2015-10-14) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.5.0...v0.6.0) + +**Merged pull requests:** + +- Convert to mspcrunch [\#17](https://github.com/sanger-pathogens/pymummer/pull/17) ([martinghunt](https://github.com/martinghunt)) + +## [v0.5.0](https://github.com/sanger-pathogens/pymummer/tree/v0.5.0) (2015-10-09) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.4.0...v0.5.0) + +**Merged pull requests:** + +- Msp crunch output [\#16](https://github.com/sanger-pathogens/pymummer/pull/16) ([martinghunt](https://github.com/martinghunt)) +- Add TravisCI support [\#15](https://github.com/sanger-pathogens/pymummer/pull/15) ([bewt85](https://github.com/bewt85)) + +## [v0.4.0](https://github.com/sanger-pathogens/pymummer/tree/v0.4.0) (2015-05-28) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.3.0...v0.4.0) + +**Merged pull requests:** + +- Expose diagdiff to nucmer [\#14](https://github.com/sanger-pathogens/pymummer/pull/14) ([martinghunt](https://github.com/martinghunt)) + +## [v0.3.0](https://github.com/sanger-pathogens/pymummer/tree/v0.3.0) (2015-05-15) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.2.0...v0.3.0) + +## [v0.2.0](https://github.com/sanger-pathogens/pymummer/tree/v0.2.0) (2015-05-15) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.1.0...v0.2.0) + +**Merged pull requests:** + +- Reverse alignments [\#13](https://github.com/sanger-pathogens/pymummer/pull/13) ([martinghunt](https://github.com/martinghunt)) +- Fix constructing alignment from promer output [\#12](https://github.com/sanger-pathogens/pymummer/pull/12) ([martinghunt](https://github.com/martinghunt)) +- Add promer option; version bump [\#11](https://github.com/sanger-pathogens/pymummer/pull/11) ([martinghunt](https://github.com/martinghunt)) + +## [v0.1.0](https://github.com/sanger-pathogens/pymummer/tree/v0.1.0) (2015-03-05) +[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.0.2...v0.1.0) + +**Merged pull requests:** + +- minor version number incremented [\#10](https://github.com/sanger-pathogens/pymummer/pull/10) ([nds](https://github.com/nds)) +- Added --nosimplify toggle to nucmer command [\#9](https://github.com/sanger-pathogens/pymummer/pull/9) ([nds](https://github.com/nds)) + +## [v0.0.2](https://github.com/sanger-pathogens/pymummer/tree/v0.0.2) (2015-02-02) +**Merged pull requests:** + +- Change to pyfastaq; add to pypi [\#8](https://github.com/sanger-pathogens/pymummer/pull/8) ([martinghunt](https://github.com/martinghunt)) +- put system call code in seprate module [\#7](https://github.com/sanger-pathogens/pymummer/pull/7) ([martinghunt](https://github.com/martinghunt)) +- Add snp\_file to list of modules [\#6](https://github.com/sanger-pathogens/pymummer/pull/6) ([martinghunt](https://github.com/martinghunt)) +- Added documentation in README file [\#5](https://github.com/sanger-pathogens/pymummer/pull/5) ([nds](https://github.com/nds)) +- Add variant calling [\#4](https://github.com/sanger-pathogens/pymummer/pull/4) ([martinghunt](https://github.com/martinghunt)) +- Added some doc lines [\#3](https://github.com/sanger-pathogens/pymummer/pull/3) ([nds](https://github.com/nds)) +- Split into separate files [\#2](https://github.com/sanger-pathogens/pymummer/pull/2) ([martinghunt](https://github.com/martinghunt)) +- Initial commit [\#1](https://github.com/sanger-pathogens/pymummer/pull/1) ([martinghunt](https://github.com/martinghunt)) + diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..4faa525 --- /dev/null +++ b/LICENSE @@ -0,0 +1,679 @@ +Copyright (c) 2015 - 2017 by Genome Research Ltd. + +This is free software, licensed under: + +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software 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But first, please read +. + diff --git a/README.md b/README.md new file mode 100644 index 0000000..cc49559 --- /dev/null +++ b/README.md @@ -0,0 +1,94 @@ +# pymummer + +Python3 wrapper for running MUMmer and parsing the output. + +[![Build Status](https://travis-ci.org/sanger-pathogens/pymummer.svg?branch=master)](https://travis-ci.org/sanger-pathogens/pymummer) +[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/pymummer/blob/master/LICENSE) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/pymummer/README.html) +[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/pymummer) + +## Contents + * [Introduction](#introduction) + * [Installation](#installation) + * [Required dependencies](#required-dependencies) + * [Homebrew/LinuxBrew](#homebrewlinuxbrew) + * [Using pip](#using-pip) + * [Running the tests](#running-the-tests) + * [Usage (for developers)](#usage-for-developers) + * [pymummer nucmer class](#pymummer-nucmer-class) + * [pymummer coords\_file class](#pymummer-coords_file-class) + * [pymummer alignment class](#pymummer-alignment-class) + * [License](#license) + * [Feedback/Issues](#feedbackissues) + +## Introduction +Runs MUMmer and parses the output. + +## Installation +pymummer has the following dependencies: + +### Required dependencies +* [MUMmer](http://mummer.sourceforge.net/manual/#installation) + +There are a number of ways to install pymummer and details are provided below. If you encounter an issue when installing pymummer please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/pymummer/issues) or email us at path-help@sanger.ac.uk. + +### Homebrew/LinuxBrew +``` +brew tap homebrew/python +brew install pymummer +``` + +### Using pip +``` +pip3 install pymummer +``` +### Running the tests +The test can be run from the top level directory: + +``` +python setup.py test +``` + +## Usage (for developers) + +Example showing how pymummer can be used to run nucmer on a fasta file and parse the output file to produce a set of alignment objects: +``` +from pymummer import coords_file, alignment, nucmer +... +runner = nucmer.Runner(reference_file, query_file, results_file) +runner.run() +file_reader = coords_file.reader(results_file) +alignments = [coord for coord in file_reader if not coord.is_self_hit()] #Remove self hits +... +``` +### pymummer nucmer class + +Wraps the `nucmer`, `delta-filter`, `show-coords` and `show-snps` commands. + +Arguments: +``` +__ref__ reference file +__query__ query file +__outfile__ output file +__min\_id__ min\_id for delta-filter command (default None) +__min\_length__ min\_length for delta-filter command (default None) +__breaklen__ breaklen for nucmer command (nucmer's default is 200) +__coords\_header__ print header in show-coords output (default True) +__maxmatch__ maxmatch for nucmer (default False) +__show\_snps__ run show-snps (default False) +__snps\_header__ print header in show-snps output (default True) +``` + +### pymummer coords_file class + +Parses the nucmer output and populate an alignment object for each hit in the output + +### pymummer alignment class + +Check attributes of a hit, swap the reference and query, check if it's a self hit and so on + +## License +pymummer is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/pymummer/blob/master/LICENSE). + +## Feedback/Issues +Please report any issues to the [issues page](https://github.com/sanger-pathogens/pymummer/issues) or email path-help@sanger.ac.uk. \ No newline at end of file diff --git a/install_dependencies.sh b/install_dependencies.sh new file mode 100644 index 0000000..35a464b --- /dev/null +++ b/install_dependencies.sh @@ -0,0 +1,69 @@ +#!/bin/bash + +set -x +set -e + +start_dir=$(pwd) + +MUMMER_VERSION="3.23" + +MUMMER_DOWNLOAD_URL="http://sourceforge.net/projects/mummer/files/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz/download" + +# Make an install location +if [ ! -d 'build' ]; then + mkdir build +fi +cd build +build_dir=$(pwd) + +# DOWNLOAD ALL THE THINGS +download () { + url=$1 + download_location=$2 + + if [ -e $download_location ]; then + echo "Skipping download of $url, $download_location already exists" + else + echo "Downloading $url to $download_location" + wget $url -O $download_location + fi +} + +download $MUMMER_DOWNLOAD_URL "mummer-${MUMMER_VERSION}.tgz" + +# Build all the things +cd $build_dir + +## Mummer +mummer_dir=$(pwd)/MUMmer${MUMMER_VERSION} +if [ ! -d $mummer_dir ]; then + tar xzf mummer-${MUMMER_VERSION}.tgz +fi +cd $mummer_dir +if [ -e "${mummer_dir}/mummer" ]; then + echo "Already built Mummer; skipping build" +else + make check + make + cd ./src/tigr + make +fi + +cd $build_dir + +# Setup environment variables +update_path () { + new_dir=$1 + export PATH=${PATH:-$new_dir} + if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then + export PATH=${new_dir}:${PATH} + fi +} + +update_path ${mummer_dir} +update_path ${mummer_dir}/src/tigr + +cd $start_dir + +set +x +set +e diff --git a/pymummer/__init__.py b/pymummer/__init__.py new file mode 100644 index 0000000..dd7bf26 --- /dev/null +++ b/pymummer/__init__.py @@ -0,0 +1,19 @@ +from pkg_resources import get_distribution + +try: + __version__ = get_distribution('pymummer').version +except: + __version__ = 'local' + + +__all__ = [ + 'alignment', + 'coords_file', + 'nucmer', + 'snp', + 'snp_file', + 'syscall', + 'variant', +] + +from pymummer import * diff --git a/pymummer/alignment.py b/pymummer/alignment.py new file mode 100644 index 0000000..15760f5 --- /dev/null +++ b/pymummer/alignment.py @@ -0,0 +1,219 @@ +import pyfastaq +from pymummer import variant + +class Error (Exception): pass + +class Alignment: + def __init__(self, line): + '''Constructs Alignment object from a line of show-coords -dTlro''' + # nucmer: + # [S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] + #1162 25768 24536 4 24607 24533 99.32 640851 24536 1 -1 ref qry [CONTAINS] + + # promer: + #[S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [% SIM] [% STP] [LEN R] [LEN Q] [FRM] [TAGS] + # 1 1398 4891054 4892445 1398 1392 89.55 93.18 0.21 1398 5349013 1 1 ref qry [CONTAINED] + + fields = line.rstrip().split('\t') + + try: + self.ref_start = int(fields[0]) - 1 + self.ref_end = int(fields[1]) - 1 + self.qry_start = int(fields[2]) - 1 + self.qry_end = int(fields[3]) - 1 + self.hit_length_ref = int(fields[4]) + self.hit_length_qry = int(fields[5]) + self.percent_identity = float(fields[6]) + + if len(fields) >= 15: # promer has more fields + self.ref_length = int(fields[9]) + self.qry_length = int(fields[10]) + self.frame = int(fields[11]) + self.ref_name = fields[13] + self.qry_name = fields[14] + else: + self.ref_length = int(fields[7]) + self.qry_length = int(fields[8]) + self.frame = int(fields[9]) + self.ref_name = fields[11] + self.qry_name = fields[12] + except: + raise Error('Error reading this nucmer line:\n' + line) + + + def __eq__(self, other): + return type(other) is type(self) and self.__dict__ == other.__dict__ + + + def __hash__(self): + return hash((self.ref_start, self.ref_end, self.qry_start, self.qry_end, self.hit_length_ref, self.hit_length_qry, self.percent_identity, self.ref_length, self.qry_length, self.frame, self.ref_name, self.qry_name)) + + + def _swap(self): + '''Swaps the alignment so that the reference becomes the query and vice-versa. Swaps their names, coordinates etc. The frame is not changed''' + self.ref_start, self.qry_start = self.qry_start, self.ref_start + self.ref_end, self.qry_end = self.qry_end, self.ref_end + self.hit_length_ref, self.hit_length_qry = self.hit_length_qry, self.hit_length_ref + self.ref_length, self.qry_length = self.qry_length, self.ref_length + self.ref_name, self.qry_name = self.qry_name, self.ref_name + + + def qry_coords(self): + '''Returns a pyfastaq.intervals.Interval object of the start and end coordinates in the query sequence''' + return pyfastaq.intervals.Interval(min(self.qry_start, self.qry_end), max(self.qry_start, self.qry_end)) + + + def ref_coords(self): + '''Returns a pyfastaq.intervals.Interval object of the start and end coordinates in the reference sequence''' + return pyfastaq.intervals.Interval(min(self.ref_start, self.ref_end), max(self.ref_start, self.ref_end)) + + + def on_same_strand(self): + '''Returns true iff the direction of the alignment is the same in the reference and the query''' + return (self.ref_start < self.ref_end) == (self.qry_start < self.qry_end) + + + def is_self_hit(self): + '''Returns true iff the alignment is of a sequence to itself: names and all coordinates are the same and 100 percent identity''' + return self.ref_name == self.qry_name \ + and self.ref_start == self.qry_start \ + and self.ref_end == self.qry_end \ + and self.percent_identity == 100 + + + def reverse_query(self): + '''Changes the coordinates as if the query sequence has been reverse complemented''' + self.qry_start = self.qry_length - self.qry_start - 1 + self.qry_end = self.qry_length - self.qry_end - 1 + + + def reverse_reference(self): + '''Changes the coordinates as if the reference sequence has been reverse complemented''' + self.ref_start = self.ref_length - self.ref_start - 1 + self.ref_end = self.ref_length - self.ref_end - 1 + + + def __str__(self): + '''Returns a tab delimited string containing the values of this alignment object''' + return '\t'.join(str(x) for x in + [self.ref_start + 1, + self.ref_end + 1, + self.qry_start + 1, + self.qry_end + 1, + self.hit_length_ref, + self.hit_length_qry, + '{0:.2f}'.format(self.percent_identity), + self.ref_length, + self.qry_length, + self.frame, + self.ref_name, + self.qry_name]) + + + def to_msp_crunch(self): + '''Returns the alignment as a line in MSPcrunch format. The columns are space-separated and are: + 1. score + 2. percent identity + 3. match start in the query sequence + 4. match end in the query sequence + 5. query sequence name + 6. subject sequence start + 7. subject sequence end + 8. subject sequence name''' + + # we don't know the alignment score. Estimate it. This approximates 1 for a match. + aln_score = int(self.percent_identity * 0.005 * (self.hit_length_ref + self.hit_length_qry)) + + return ' '.join(str(x) for x in [ + aln_score, + '{0:.2f}'.format(self.percent_identity), + self.qry_start + 1, + self.qry_end + 1, + self.qry_name, + self.ref_start + 1, + self.ref_end + 1, + self.ref_name + ]) + + + def intersects_variant(self, var): + var_ref_coords = sorted([var.ref_start, var.ref_end]) + var_ref_coords = pyfastaq.intervals.Interval(var_ref_coords[0], var_ref_coords[1]) + var_qry_coords = sorted([var.qry_start, var.qry_end]) + var_qry_coords = pyfastaq.intervals.Interval(var_qry_coords[0], var_qry_coords[1]) + return var_ref_coords.intersects(self.ref_coords()) and var_qry_coords.intersects(self.qry_coords()) + + + def qry_coords_from_ref_coord(self, ref_coord, variant_list): + '''Given a reference position and a list of variants ([variant.Variant]), + works out the position in the query sequence, accounting for indels. + Returns a tuple: (position, True|False), where second element is whether + or not the ref_coord lies in an indel. If it is, then + returns the corresponding start position + of the indel in the query''' + if self.ref_coords().distance_to_point(ref_coord) > 0: + raise Error('Cannot get query coord in qry_coords_from_ref_coord because given ref_coord ' + str(ref_coord) + ' does not lie in nucmer alignment:\n' + str(self)) + + indel_variant_indexes = [] + + for i in range(len(variant_list)): + if variant_list[i].var_type not in {variant.INS, variant.DEL}: + continue + if not self.intersects_variant(variant_list[i]): + continue + if variant_list[i].ref_start <= ref_coord <= variant_list[i].ref_end: + return variant_list[i].qry_start, True + elif variant_list[i].ref_start < ref_coord: + indel_variant_indexes.append(i) + + distance = ref_coord - min(self.ref_start, self.ref_end) + + for i in indel_variant_indexes: + if variant_list[i].var_type == variant.INS: + distance += len(variant_list[i].qry_base) + else: + assert variant_list[i].var_type == variant.DEL + distance -= len(variant_list[i].ref_base) + + if self.on_same_strand(): + return min(self.qry_start, self.qry_end) + distance, False + else: + return max(self.qry_start, self.qry_end) - distance, False + + + def ref_coords_from_qry_coord(self, qry_coord, variant_list): + '''Given a qryerence position and a list of variants ([variant.Variant]), + works out the position in the ref sequence, accounting for indels. + Returns a tuple: (position, True|False), where second element is whether + or not the qry_coord lies in an indel. If it is, then + returns the corresponding start position + of the indel in the ref''' + if self.qry_coords().distance_to_point(qry_coord) > 0: + raise Error('Cannot get ref coord in ref_coords_from_qry_coord because given qry_coord ' + str(qry_coord) + ' does not lie in nucmer alignment:\n' + str(self)) + + indel_variant_indexes = [] + + for i in range(len(variant_list)): + if variant_list[i].var_type not in {variant.INS, variant.DEL}: + continue + if not self.intersects_variant(variant_list[i]): + continue + if variant_list[i].qry_start <= qry_coord <= variant_list[i].qry_end: + return variant_list[i].ref_start, True + elif variant_list[i].qry_start < qry_coord: + indel_variant_indexes.append(i) + + distance = qry_coord - min(self.qry_start, self.qry_end) + + for i in indel_variant_indexes: + if variant_list[i].var_type == variant.DEL: + distance += len(variant_list[i].ref_base) + else: + assert variant_list[i].var_type == variant.INS + distance -= len(variant_list[i].qry_base) + + if self.on_same_strand(): + return min(self.ref_start, self.ref_end) + distance, False + else: + return max(self.ref_start, self.ref_end) - distance, False + diff --git a/pymummer/coords_file.py b/pymummer/coords_file.py new file mode 100644 index 0000000..27b09c9 --- /dev/null +++ b/pymummer/coords_file.py @@ -0,0 +1,47 @@ +import pyfastaq +from pymummer import alignment + +class Error (Exception): pass + +def reader(fname): + '''Helper function to open the results file (coords file) and create alignment objects with the values in it''' + f = pyfastaq.utils.open_file_read(fname) + + for line in f: + if line.startswith('[') or (not '\t' in line): + continue + + yield alignment.Alignment(line) + + pyfastaq.utils.close(f) + + +def convert_to_msp_crunch(infile, outfile, ref_fai=None, qry_fai=None): + '''Converts a coords file to a file in MSPcrunch format (for use with ACT, most likely). + ACT ignores sequence names in the crunch file, and just looks at the numbers. + To make a compatible file, the coords all must be shifted appropriately, which + can be done by providing both the ref_fai and qry_fai options. + Both or neither of these must be used, otherwise an error will be thrown.''' + fai_files = {ref_fai, qry_fai} + if None in fai_files and len(fai_files) != 1: + print(fai_files) + raise Error('Error in convert_to_msp_crunch. Must use both of ref_fai and qry_fai, or neither of them') + + if ref_fai is not None: + assert qry_fai is not None + ref_offsets = pyfastaq.tasks.length_offsets_from_fai(ref_fai) + qry_offsets = pyfastaq.tasks.length_offsets_from_fai(qry_fai) + + file_reader = reader(infile) + f_out = pyfastaq.utils.open_file_write(outfile) + + for aln in file_reader: + if ref_fai is not None: + aln.ref_start += ref_offsets[aln.ref_name] + aln.ref_end += ref_offsets[aln.ref_name] + aln.qry_start += qry_offsets[aln.qry_name] + aln.qry_end += qry_offsets[aln.qry_name] + + print(aln.to_msp_crunch(), file=f_out) + + pyfastaq.utils.close(f_out) diff --git a/pymummer/nucmer.py b/pymummer/nucmer.py new file mode 100644 index 0000000..5c7d0b9 --- /dev/null +++ b/pymummer/nucmer.py @@ -0,0 +1,147 @@ +import os +import tempfile +import shutil +import pyfastaq +from pymummer import syscall + +class Error (Exception): pass + + +class Runner: + '''Handy reference for all the arguments needed for nucmer, delta-filter, show-coords, show-snps''' + def __init__( + self, + ref, + query, + outfile, + min_id=None, + min_length=None, + breaklen=None, + coords_header=True, + diagdiff=None, + diagfactor=None, + maxgap=None, + maxmatch=False, + mincluster=None, + simplify=True, + show_snps=False, + snps_header=True, + verbose=False, + promer=False, + show_snps_C=True, + ): + self.qry = query + self.ref = ref + self.outfile = outfile + self.min_id = min_id + self.min_length = min_length + self.breaklen = breaklen + self.diagdiff = diagdiff + self.diagfactor = diagfactor + self.coords_header = coords_header + self.maxgap = maxgap + self.maxmatch = maxmatch + self.mincluster = mincluster + self.simplify = simplify + self.show_snps = show_snps + self.snps_header = snps_header + self.verbose = verbose + self.use_promer = promer + self.show_snps_C = show_snps_C + + + def _nucmer_command(self, ref, qry, outprefix): + '''Construct the nucmer command''' + if self.use_promer: + command = 'promer' + else: + command = 'nucmer' + + command += ' -p ' + outprefix + + if self.breaklen is not None: + command += ' -b ' + str(self.breaklen) + + if self.diagdiff is not None and not self.use_promer: + command += ' -D ' + str(self.diagdiff) + + if self.diagfactor: + command += ' -d ' + str(self.diagfactor) + + if self.maxgap: + command += ' -g ' + str(self.maxgap) + + if self.maxmatch: + command += ' --maxmatch' + + if self.mincluster is not None: + command += ' -c ' + str(self.mincluster) + + if not self.simplify and not self.use_promer: + command += ' --nosimplify' + + return command + ' ' + ref + ' ' + qry + + + def _delta_filter_command(self, infile, outfile): + '''Construct delta-filter command''' + command = 'delta-filter' + + if self.min_id is not None: + command += ' -i ' + str(self.min_id) + + if self.min_length is not None: + command += ' -l ' + str(self.min_length) + + return command + ' ' + infile + ' > ' + outfile + + + def _show_coords_command(self, infile, outfile): + '''Construct show-coords command''' + command = 'show-coords -dTlro' + + if not self.coords_header: + command += ' -H' + + return command + ' ' + infile + ' > ' + outfile + + + def _show_snps_command(self, infile, outfile): + command = 'show-snps -T' + ('C' if self.show_snps_C else '') + 'lr' + + if not self.snps_header: + command += ' -H' + + return command + ' ' + infile + ' > ' + outfile + + + def _write_script(self, script_name, ref, qry, outfile): + '''Write commands into a bash script''' + f = pyfastaq.utils.open_file_write(script_name) + print(self._nucmer_command(ref, qry, 'p'), file=f) + print(self._delta_filter_command('p.delta', 'p.delta.filter'), file=f) + print(self._show_coords_command('p.delta.filter', outfile), file=f) + if self.show_snps: + print(self._show_snps_command('p.delta.filter', outfile + '.snps'), file=f) + pyfastaq.utils.close(f) + + + def run(self): + ''' + Change to a temp directory + Run bash script containing commands + Place results in specified output file + Clean up temp directory + ''' + qry = os.path.abspath(self.qry) + ref = os.path.abspath(self.ref) + outfile = os.path.abspath(self.outfile) + tmpdir = tempfile.mkdtemp(prefix='tmp.run_nucmer.', dir=os.getcwd()) + original_dir = os.getcwd() + os.chdir(tmpdir) + script = 'run_nucmer.sh' + self._write_script(script, ref, qry, outfile) + syscall.run('bash ' + script, verbose=self.verbose) + os.chdir(original_dir) + shutil.rmtree(tmpdir) + diff --git a/pymummer/snp.py b/pymummer/snp.py new file mode 100644 index 0000000..92f4672 --- /dev/null +++ b/pymummer/snp.py @@ -0,0 +1,45 @@ +class Error (Exception): pass + + +class Snp: + def __init__(self, line): + # Without the -C option to show-snps, looks like this: + #[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS] + #187 A C 269 187 187 654 853 1 1 ref_name qry_name + + # With the -C option to show-snps, looks like this: + #[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [R] [Q] [LEN R] [LEN Q] [FRM] [TAGS] + #187 A C 269 187 187 0 0 654 853 1 1 ref_name qry_name + try: + l = line.rstrip().split('\t') + self.ref_pos = int(l[0]) - 1 + self.ref_base = l[1] + self.qry_base = l[2] + self.qry_pos = int(l[3]) - 1 + self.ref_length = int(l[-6]) + self.qry_length = int(l[-5]) + self.reverse = {'1': False, '-1': True}[l[-3]] + self.ref_name = l[-2] + self.qry_name = l[-1] + except: + raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line) + + + def __eq__(self, other): + return type(other) is type(self) and self.__dict__ == other.__dict__ + + + def __str__(self): + return '\t'.join([str(x) for x in [ + self.ref_pos + 1, + self.ref_base, + self.qry_base, + self.qry_pos + 1, + self.ref_length, + self.qry_length, + '-1' if self.reverse else '1', + self.ref_name, + self.qry_name + ]]) + + diff --git a/pymummer/snp_file.py b/pymummer/snp_file.py new file mode 100644 index 0000000..9386f5c --- /dev/null +++ b/pymummer/snp_file.py @@ -0,0 +1,24 @@ +import pyfastaq +from pymummer import snp, variant + +def reader(fname): + f = pyfastaq.utils.open_file_read(fname) + + for line in f: + if line.startswith('[') or (not '\t' in line): + continue + + yield snp.Snp(line) + + pyfastaq.utils.close(f) + + +def get_all_variants(fname): + variants = [] + fr = reader(fname) + for nucmer_snp in fr: + if len(variants) == 0 or not variants[-1].update_indel(nucmer_snp): + variants.append(variant.Variant(nucmer_snp)) + + return variants + diff --git a/pymummer/syscall.py b/pymummer/syscall.py new file mode 100644 index 0000000..4764653 --- /dev/null +++ b/pymummer/syscall.py @@ -0,0 +1,30 @@ +import os +import sys +import subprocess + +class Error (Exception): pass + + +def decode(x): + try: + s = x.decode() + except: + return x + return s + + +def run(cmd, verbose=False): + if verbose: + print('Running command:', cmd, flush=True) + try: + output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) + except subprocess.CalledProcessError as error: + print('The following command failed with exit code', error.returncode, file=sys.stderr) + print(cmd, file=sys.stderr) + print('\nThe output was:\n', file=sys.stderr) + print(error.output.decode(), file=sys.stderr) + raise Error('Error running command:', cmd) + + if verbose: + print(decode(output)) + diff --git a/pymummer/tests/alignment_test.py b/pymummer/tests/alignment_test.py new file mode 100644 index 0000000..5240e81 --- /dev/null +++ b/pymummer/tests/alignment_test.py @@ -0,0 +1,333 @@ +import unittest +import os +import pyfastaq +from pymummer import alignment, snp, variant + +modules_dir = os.path.dirname(os.path.abspath(alignment.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + +class TestNucmer(unittest.TestCase): + def test_init_nucmer(self): + '''test __init__ nucmer''' + line = '\t'.join(['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry', '[FOO]']) + a = alignment.Alignment(line) + self.assertEqual(a.ref_start, 0) + self.assertEqual(a.ref_end, 99) + self.assertEqual(a.qry_start, 1) + self.assertEqual(a.qry_end, 199) + self.assertEqual(a.hit_length_ref, 101) + self.assertEqual(a.hit_length_qry, 202) + self.assertEqual(a.percent_identity, 42.42) + self.assertEqual(a.ref_length, 123) + self.assertEqual(a.qry_length, 456) + self.assertEqual(a.frame, -1) + self.assertEqual(a.ref_name, 'ref') + self.assertEqual(a.qry_name, 'qry') + + + def test_init_promer(self): + '''test __init__ promer''' + line = '\t'.join(['1', '1398', '4891054', '4892445', '1398', '1392', '89.55', '93.18', '0.21', '1398', '5349013', '1', '1', 'ref', 'qry', '[CONTAINED]']) + + a = alignment.Alignment(line) + self.assertEqual(a.ref_start, 0) + self.assertEqual(a.ref_end, 1397) + self.assertEqual(a.qry_start, 4891053) + self.assertEqual(a.qry_end, 4892444) + self.assertEqual(a.hit_length_ref, 1398) + self.assertEqual(a.hit_length_qry, 1392) + self.assertEqual(a.percent_identity, 89.55) + self.assertEqual(a.ref_length, 1398) + self.assertEqual(a.qry_length, 5349013) + self.assertEqual(a.frame, 1) + self.assertEqual(a.ref_name, 'ref') + self.assertEqual(a.qry_name, 'qry') + + + def test_swap(self): + ''' test swap''' + l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry'] + l_out = ['2', '200', '1', '100', '202', '101', '42.42', '456', '123', '-1', '0', 'qry', 'ref'] + a_in = alignment.Alignment('\t'.join(l_in)) + a_in._swap() + self.assertEqual(a_in, alignment.Alignment('\t'.join(l_out))) + a_in._swap() + self.assertEqual(a_in, alignment.Alignment('\t'.join(l_in))) + + + def test_qry_coords(self): + '''Test qry_coords''' + hits = ['\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'qry']), + '\t'.join(['1', '101', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'qry']) + ] + for h in hits: + a = alignment.Alignment(h) + self.assertEqual(pyfastaq.intervals.Interval(0,99), a.qry_coords()) + + + def test_ref_coords(self): + '''Test ref_coords''' + hits = ['\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), + '\t'.join(['100', '1', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']) + ] + for h in hits: + a = alignment.Alignment(h) + self.assertEqual(pyfastaq.intervals.Interval(0,99), a.ref_coords()) + + + def test_on_same_strand(self): + '''test on_same_strand''' + self.assertTrue(alignment.Alignment('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) + self.assertTrue(alignment.Alignment('\t'.join(['100', '1', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) + self.assertFalse(alignment.Alignment('\t'.join(['1', '100', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) + self.assertFalse(alignment.Alignment('\t'.join(['100', '1', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])).on_same_strand()) + + + def test_is_self_hit(self): + '''Test is_self_hit''' + tests = [('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), True), + ('\t'.join(['1', '101', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), False), + ('\t'.join(['2', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']), False), + ('\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref2']), False), + ('\t'.join(['1', '100', '1', '100', '100', '100', '99.9', '1000', '1000', '1', '1', 'ref', 'ref']), False), + ] + + for t in tests: + a = alignment.Alignment(t[0]) + self.assertEqual(a.is_self_hit(), t[1]) + + + def test_reverse_reference(self): + '''Test reverse_reference''' + aln = alignment.Alignment('\t'.join(['100', '142', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) + expected = alignment.Alignment('\t'.join(['51', '9', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) + aln.reverse_reference() + self.assertEqual(expected, aln) + + + def test_reverse_query(self): + '''Test reverse_query''' + aln = alignment.Alignment('\t'.join(['100', '142', '1', '42', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) + expected = alignment.Alignment('\t'.join(['100', '142', '100', '59', '43', '42', '100.00', '150', '100', '1', '1', 'ref', 'qry'])) + aln.reverse_query() + self.assertEqual(expected, aln) + + + def test_str(self): + '''Test __str__''' + l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry'] + # the 10th column (counting from zero) is ignored and so not output by __str__ + l_out = l_in[:10] + l_in[11:] + a = alignment.Alignment('\t'.join(l_in)) + self.assertEqual(str(a), '\t'.join(l_out)) + + + def test_to_msp_crunch(self): + '''Test to_msp_crunch''' + l_in = ['100', '110', '1', '10', '10', '11', '80.00', '123', '456', '-1', '0', 'ref', 'qry'] + a = alignment.Alignment('\t'.join(l_in)) + expected = '8 80.00 1 10 qry 100 110 ref' + self.assertEqual(expected, a.to_msp_crunch()) + + + def test_intersects_variant(self): + 'Test intersects_variant''' + snp0 = snp.Snp('100\tA\t.\t600\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry') #100 in ref, 600 in qry + indel = variant.Variant(snp0) + + aln1 = alignment.Alignment('100\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry') + aln2 = alignment.Alignment('101\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry') + aln3 = alignment.Alignment('100\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry') + aln4 = alignment.Alignment('101\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry') + + self.assertTrue(aln1.intersects_variant(indel)) + self.assertFalse(aln2.intersects_variant(indel)) + self.assertFalse(aln3.intersects_variant(indel)) + self.assertFalse(aln4.intersects_variant(indel)) + + + def test_qry_coords_from_ref_coord_test_bad_ref_coord(self): + '''Test qry_coords_from_ref_coord with bad ref coords''' + aln = alignment.Alignment('\t'.join(['100', '200', '1', '100', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) + with self.assertRaises(alignment.Error): + got = aln.qry_coords_from_ref_coord(98, []) + + with self.assertRaises(alignment.Error): + got = aln.qry_coords_from_ref_coord(200, []) + + + def test_qry_coords_from_ref_coord_test_same_strand(self): + '''Test qry_coords_from_ref_coord on same strand''' + aln = alignment.Alignment('\t'.join(['100', '200', '1', '101', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) + snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # snp + snp0 = variant.Variant(snp0) + snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + del1 = variant.Variant(snp1) + del2 = variant.Variant(snp1) + self.assertTrue(del2.update_indel(snp2)) + snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + ins1 = variant.Variant(snp3) + ins2 = variant.Variant(snp3) + self.assertTrue(ins2.update_indel(snp4)) + self.assertTrue(ins2.update_indel(snp5)) + + tests = [ + (99, [], (0, False)), + (100, [], (1, False)), + (199, [], (100, False)), + (119, [del1], (20, False)), + (149, [], (50, False)), + (149, [del1], (49, False)), + (149, [del2], (48, False)), + (159, [], (60, False)), + (159, [ins1], (61, False)), + (159, [ins2], (63, False)), + (159, [del1, ins1], (60, False)), + (159, [del1, ins2], (62, False)), + (159, [del2, ins1], (59, False)), + (159, [del2, ins2], (61, False)), + (139, [del1], (39, True)), + (139, [snp0], (40, False)), + (149, [ins1], (49, True)), + ] + + for ref_coord, variant_list, expected in tests: + got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) + self.assertEqual(expected, got) + # if we reverse the direction of hit in query and reference, should get the same answer + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) + self.assertEqual(expected, got) + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + + + def test_qry_coords_from_ref_coord_test_different_strand(self): + '''Test qry_coords_from_ref_coord on different strand''' + aln = alignment.Alignment('\t'.join(['100', '200', '101', '1', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) + snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # snp + snp0 = variant.Variant(snp0) + snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + del1 = variant.Variant(snp1) + del2 = variant.Variant(snp1) + self.assertTrue(del2.update_indel(snp2)) + snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + ins1 = variant.Variant(snp3) + ins2 = variant.Variant(snp3) + self.assertTrue(ins2.update_indel(snp4)) + self.assertTrue(ins2.update_indel(snp5)) + + tests = [ + (99, [], (100, False)), + (100, [], (99, False)), + (199, [], (0, False)), + (119, [], (80, False)), + (119, [del1], (80, False)), + (149, [], (50, False)), + (149, [del1], (51, False)), + (149, [del2], (52, False)), + (159, [], (40, False)), + (159, [ins1], (39, False)), + (159, [ins2], (37, False)), + (159, [del1, ins1], (40, False)), + (159, [del1, ins2], (38, False)), + (159, [del2, ins1], (41, False)), + (159, [del2, ins2], (39, False)), + (139, [del1], (39, True)), + (139, [snp0], (60, False)), + (149, [ins1], (49, True)), + ] + + for ref_coord, variant_list, expected in tests: + got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) + self.assertEqual(expected, got) + # if we reverse the direction of hit in query and reference, should get the same answer + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) + self.assertEqual(expected, got) + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + + + def test_qry_coords_from_ref_coord_when_variant_not_in_nucmer_match(self): + '''Test ref_coords_from_qry_coord when variant not in nucmer match''' + aln = alignment.Alignment('1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry') + snp0 = snp.Snp('127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry') + indel = variant.Variant(snp0) + self.assertEqual((595, False), aln.qry_coords_from_ref_coord(0, [])) + self.assertEqual((595, False), aln.qry_coords_from_ref_coord(0, [indel])) + self.assertEqual((995, False), aln.qry_coords_from_ref_coord(400, [])) + self.assertEqual((995, False), aln.qry_coords_from_ref_coord(400, [indel])) + self.assertEqual((1200, False), aln.qry_coords_from_ref_coord(605, [])) + self.assertEqual((1200, False), aln.qry_coords_from_ref_coord(605, [indel])) + + + def test_ref_coords_from_qry_coord_test_same_strand(self): + '''Test ref_coords_from_qry_coord on same strand''' + aln = alignment.Alignment('\t'.join(['1', '101', '100', '200', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry'])) + snp0 = snp.Snp('\t'.join(['40', 'T', 'A', '140', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # snp + snp0 = variant.Variant(snp0) + snp1 = snp.Snp('\t'.join(['40', '.', 'A', '140', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + snp2 = snp.Snp('\t'.join(['40', '.', 'C', '141', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref + del1 = variant.Variant(snp1) + del2 = variant.Variant(snp1) + self.assertTrue(del2.update_indel(snp2)) + snp3 = snp.Snp('\t'.join(['50', 'A', '.', '150', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + snp4 = snp.Snp('\t'.join(['51', 'C', '.', '150', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + snp5 = snp.Snp('\t'.join(['52', 'G', '.', '150', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry + ins1 = variant.Variant(snp3) + ins2 = variant.Variant(snp3) + self.assertTrue(ins2.update_indel(snp4)) + self.assertTrue(ins2.update_indel(snp5)) + + tests = [ + (99, [], (0, False)), + (100, [], (1, False)), + (199, [], (100, False)), + (119, [del1], (20, False)), + (149, [], (50, False)), + (149, [del1], (49, False)), + (149, [del2], (48, False)), + (159, [], (60, False)), + (159, [ins1], (61, False)), + (159, [ins2], (63, False)), + (159, [del1, ins1], (60, False)), + (159, [del1, ins2], (62, False)), + (159, [del2, ins1], (59, False)), + (159, [del2, ins2], (61, False)), + (139, [del1], (39, True)), + (139, [snp0], (40, False)), + (149, [ins1], (49, True)), + ] + + for qry_coord, variant_list, expected in tests: + got = aln.ref_coords_from_qry_coord(qry_coord, variant_list) + self.assertEqual(expected, got) + # if we reverse the direction of hit in query and qryerence, should get the same answer + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + got = aln.ref_coords_from_qry_coord(qry_coord, variant_list) + self.assertEqual(expected, got) + aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start + aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start + + + def test_ref_coords_from_qry_coord_when_variant_not_in_nucmer_match(self): + '''Test ref_coords_from_qry_coord when variant not in nucmer match''' + aln = alignment.Alignment('1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry') + snp0 = snp.Snp('127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry') + indel = variant.Variant(snp0) + self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [])) + self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [indel])) + self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [])) + self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [indel])) + self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [])) + self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [indel])) diff --git a/pymummer/tests/coords_file_test.py b/pymummer/tests/coords_file_test.py new file mode 100644 index 0000000..b3ad26a --- /dev/null +++ b/pymummer/tests/coords_file_test.py @@ -0,0 +1,51 @@ +import unittest +import os +import filecmp +from pymummer import coords_file, alignment + +modules_dir = os.path.dirname(os.path.abspath(coords_file.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + +class TestCoordsFile(unittest.TestCase): + def test_coords_file(self): + '''test coords_file''' + expected = [ + '\t'.join(['61', '900', '1', '840', '840', '840', '99.76', '1000', '840', '1', '1', 'test_ref1', 'test_qry1', '[CONTAINS]']), + '\t'.join(['62', '901', '2', '841', '841', '850', '99.66', '999', '839', '1', '1', 'test_ref2', 'test_qry2', '[CONTAINS]']), + '\t'.join(['63', '902', '3', '842', '842', '860', '99.56', '998', '838', '1', '1', 'test_ref3', 'test_qry3', '[CONTAINS]']) + ] + expected = [alignment.Alignment(x) for x in expected] + + infiles = [os.path.join(data_dir, 'coords_file_test_with_header.coords'), os.path.join(data_dir, 'coords_file_test_no_header.coords')] + + for fname in infiles: + fr = coords_file.reader(fname) + alignments = [x for x in fr] + self.assertEqual(alignments, expected) + + + def test_convert_to_msp_crunch_no_offset(self): + '''Test convert_to_msp_crunch with no offsets''' + infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords') + expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.no_offset.crunch') + tmpfile = 'tmp.test_convert_to_msp_crunch_no_offset.crunch' + coords_file.convert_to_msp_crunch(infile, tmpfile) + self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) + os.unlink(tmpfile) + + + def test_convert_to_msp_crunch_with_offset(self): + '''Test convert_to_msp_crunch with offsets''' + infile = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.coords') + ref_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.ref.fa.fai') + qry_fai = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.qry.fa.fai') + expected = os.path.join(data_dir, 'coords_file_test_convert_to_msp_crunch.with_offset.crunch') + tmpfile = 'tmp.test_convert_to_msp_crunch_with_offset.crunch' + + with self.assertRaises(coords_file.Error): + coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai) + coords_file.convert_to_msp_crunch(infile, tmpfile, qry_fai=qry_fai) + + coords_file.convert_to_msp_crunch(infile, tmpfile, ref_fai=ref_fai, qry_fai=qry_fai) + self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) + os.unlink(tmpfile) diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords new file mode 100644 index 0000000..9e44934 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords @@ -0,0 +1,7 @@ +/Users/mh12/sanger-pathogens/pymummer/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa /Users/mh12/sanger-pathogens/pymummer/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa +NUCMER + +[S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] +1 420 1 420 420 420 99.76 420 420 1 1 ref1 qry1 [IDENTITY] +1 480 1 479 480 479 99.58 480 479 1 1 ref2 qry2 [IDENTITY] +61 420 1 360 360 360 99.44 500 360 1 1 ref3 qry3 [CONTAINS] diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch new file mode 100644 index 0000000..9b1eff9 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch @@ -0,0 +1,3 @@ +418 99.76 1 420 qry1 1 420 ref1 +477 99.58 1 479 qry2 1 480 ref2 +357 99.44 1 360 qry3 61 420 ref3 diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa new file mode 100644 index 0000000..c9ffa23 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa @@ -0,0 +1,24 @@ +>qry1 +AACTTTCATACTGTAGTTATTGGCATCGTTGTAAAATTGCTCACCACGTCGCTCGTTCAT +GATAATCTAAAGATCGCTAACGATTACTACCGGCAGCGGTTTATACGGACCAATCGTTGG +TTCATTTTAATGTAGACCCAGAAATCGACTGCATTTCTGCAGCCCGGCCCGACGTGTTGA +ACGGATGATCTTAGACAGAACGTCCTTGGGTCTATATCCGGCCACATATTTATTGGGCAG +GGGAGTCAATTGGGGGCGTACCGAAATATCGTCTTTACGAGCGTCGGTGACGCACATGAC +ATGGTCGACCCATAGCCTCAGCTTCTAGACGGTTGCACCAGCGCAAGACAAAACTCTCAA +TTTTGTCTGGGTACCGAGATTGCGGAACCGGGGATATTGTAGAGCGGTGCACACGGCCTT +>qry2 +CTAGCGCAAGACCGACTCTGATTCATGGAGACAGGGCCAGACAGGGAAACGAGATTGAGC +GATGCTGTCATTTTCGTAACGAGGATTGGTCGGGGACCGAGATCGTACACGTCTCCGAGC +CCCCACAGTCGAGTACAAATGGCTTAATTTACTGACTTCTTCCTGTTACCGGCATGGTAT +GCTGAGCCTGGCCCGCTCACTATTGGATATAGCCTGTGCGCTGGCGTACCGCTGTTCTAC +CGGTTCCTCTTGAGGGTCAAAGGCCGGCTACCATCGTTAACTTATTAGCTTAGAGTAATG +TAGGTTACGTGACGCTGGCCGGTTAGCGTTTCGAAGGATCGCAGGACTATAGTCAAAACT +CGTGGACTTCTACCAGAACTATCGATGTTCACGATGACTACGTTCCTTCCGAATATTACA +GTAAGGGATAGTCATGCCGGTTTAACATCATCTGTGTGTACGCAATGCAGTTTGGCACA +>qry3 +AGGTGCGACAGGATCTAACACCTGTACAGTAAGAAAGGGGCATATGATCGACCCCGGTTG +CTCGTATGATAATCCCATTATTGTTATCTGAGGATCGTTATGCGGCAGTTCTAGTCCGAT +AAAAGTTAGGTGAGTTGTGTTGGTAATCCTTCTCTAGGAGGCCTGGCGACTCCACTGAGC +CCAGCGATGGGAGAGCTGGTCCCCCCAATATCGTGACTGAATTGGTAAGGTAGATATCTC +CCAGATAGCCGCATACCGTCTGGCACCGTCGACCGAAAGAAATGTTCGCCTTGGCATGCT +CAGATTGCATCTATACTTACTTGTATAGAACTGCCCGCGCCACCCAGAAGACAAACTAAT diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai new file mode 100644 index 0000000..2b20707 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai @@ -0,0 +1,3 @@ +qry1 420 6 60 61 +qry2 479 439 60 61 +qry3 360 932 60 61 diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa new file mode 100644 index 0000000..2f0afca --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa @@ -0,0 +1,27 @@ +>ref1 +AACTTTCATACTGTAGTTATTGGCATCGTTGTAAAATTGCTCACCACGTCGCTCGTTCAT +GATAATCTAAAGATCGCTAACGATTACTACCGGCAGCGGTTTATACGGACCAATCGTTGG +TTCATTTTAATGTAGACCCAGAAATCGACTGCATTTCTGCAGCCCGGCCCGACGTGTTGA +ACGGATGATCTTAGACAGAACGTCCTTGGGTCTATATCCGGCCACATATTTATTGGGCAG +GGGTGTCAATTGGGGGCGTACCGAAATATCGTCTTTACGAGCGTCGGTGACGCACATGAC +ATGGTCGACCCATAGCCTCAGCTTCTAGACGGTTGCACCAGCGCAAGACAAAACTCTCAA +TTTTGTCTGGGTACCGAGATTGCGGAACCGGGGATATTGTAGAGCGGTGCACACGGCCTT +>ref2 +CTAGCGCAAGACCGACTCTGATTCATGGAGACAGGGCCAGACAGGGAAACGAGATTGAGC +GATGCTGTCATTTTCGTAACGAGGATTGGTCGGGGACCGAGATCGTACACGTCTCCGAGC +CCCCACAGTCGAGTACAAATGGCTTAATTTACTGACTTCTTCCTGTTACCGGCATGGTAT +GCTGAGCCTGGCCCGCTCACTATTGGATATAGCCTGTGCGCTGGCGTACCGCTGTTCTAC +CGGTACCTCTTGAGGGTCAAAGGCCGGCTACCATCGTTAACTTATTAGCTTAGAGTAATG +TAGGTTACGTGACGCTGGCCGGTTAGCGTTTCGAAGGATCGCAGGACTATAGTCAAAACT +CGTGGACTTCTACCAGAACTATCGATGTTCACGATGACTACGTTCCTTCCGAATATTACA +GTATAGGGATAGTCATGCCGGTTTAACATCATCTGTGTGTACGCAATGCAGTTTGGCACA +>ref3 +ATTCAACGGGTAGGGTCATCAGATTTTTAGTACGAACGAACAATTCCCCATTCAATTCCG +AGGTGCGACAGGATCTAACACCTGTACAGTAAGAAAGGGGCATATGATCGACCCCGGTTG +CTCGTATGATAATCCCATTATTGTTATCTGAGGATCGTTATGCGGCAGTTCTAGTCCGAT +CCAAGTTAGGTGAGTTGTGTTGGTAATCCTTCTCTAGGAGGCCTGGCGACTCCACTGAGC +CCAGCGATGGGAGAGCTGGTCCCCCCAATATCGTGACTGAATTGGTAAGGTAGATATCTC +CCAGATAGCCGCATACCGTCTGGCACCGTCGACCGAAAGAAATGTTCGCCTTGGCATGCT +CAGATTGCATCTATACTTACTTGTATAGAACTGCCCGCGCCACCCAGAAGACAAACTAAT +TTATTGTCGCTCAAACCTGTTTAGTTAATTCACCTTTGTAACCAGCTTACCCTCAATTGC +GTATGTAACTCCTTGGCTGC diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai new file mode 100644 index 0000000..da15e5d --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai @@ -0,0 +1,3 @@ +ref1 420 6 60 61 +ref2 480 439 60 61 +ref3 500 933 60 61 diff --git a/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch new file mode 100644 index 0000000..a0a6bd8 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch @@ -0,0 +1,3 @@ +418 99.76 1 420 qry1 1 420 ref1 +477 99.58 421 899 qry2 421 900 ref2 +357 99.44 900 1259 qry3 961 1320 ref3 diff --git a/pymummer/tests/data/coords_file_test_no_header.coords b/pymummer/tests/data/coords_file_test_no_header.coords new file mode 100644 index 0000000..aa09fe2 --- /dev/null +++ b/pymummer/tests/data/coords_file_test_no_header.coords @@ -0,0 +1,3 @@ +61 900 1 840 840 840 99.76 1000 840 1 1 test_ref1 test_qry1 [CONTAINS] +62 901 2 841 841 850 99.66 999 839 1 1 test_ref2 test_qry2 [CONTAINS] +63 902 3 842 842 860 99.56 998 838 1 1 test_ref3 test_qry3 [CONTAINS] diff --git a/pymummer/tests/data/coords_file_test_with_header.coords b/pymummer/tests/data/coords_file_test_with_header.coords new file mode 100644 index 0000000..f3b61dd --- /dev/null +++ b/pymummer/tests/data/coords_file_test_with_header.coords @@ -0,0 +1,7 @@ +/path/to/ref.fa /path/to/query.fa +NUCMER + +[S1] [E1] [S2] [E2] [LEN 1] [LEN 2] [% IDY] [LEN R] [LEN Q] [FRM] [TAGS] +61 900 1 840 840 840 99.76 1000 840 1 1 test_ref1 test_qry1 [CONTAINS] +62 901 2 841 841 850 99.66 999 839 1 1 test_ref2 test_qry2 [CONTAINS] +63 902 3 842 842 860 99.56 998 838 1 1 test_ref3 test_qry3 [CONTAINS] diff --git a/pymummer/tests/data/nucmer_test_out.coords b/pymummer/tests/data/nucmer_test_out.coords new file mode 100644 index 0000000..1c38468 --- /dev/null +++ b/pymummer/tests/data/nucmer_test_out.coords @@ -0,0 +1 @@ +61 900 1 840 840 840 99.76 1000 840 1 1 test_ref test_qry [CONTAINS] diff --git a/pymummer/tests/data/nucmer_test_out.coords.snps b/pymummer/tests/data/nucmer_test_out.coords.snps new file mode 100644 index 0000000..bc36e4e --- /dev/null +++ b/pymummer/tests/data/nucmer_test_out.coords.snps @@ -0,0 +1,2 @@ +436 C . 375 2 375 1000 840 1 1 test_ref test_qry +438 . G 378 2 378 1000 840 1 1 test_ref test_qry diff --git a/pymummer/tests/data/nucmer_test_qry.fa b/pymummer/tests/data/nucmer_test_qry.fa new file mode 100644 index 0000000..294ad9a --- /dev/null +++ b/pymummer/tests/data/nucmer_test_qry.fa @@ -0,0 +1,15 @@ +>test_qry +GTAATCAAATAATCCACCGGATGAGGTATTTTCTCATCGGGGTGACTCTAACCACATCGT +GTTTCTTCCTGAAGGCTCTAAGATGTCATGAGAACTCTTACTGTCTAGCTGAGGGGCTTG +TGCACAACACTAGGATTGTGTCTTATGCTCTATTGGACAGCGAAAACTGCTGAAATTAAC +GGGCCGTAACATACTATATTCTTCAAACCGAATTAACGTTCAGCCCCCGCTTGATTGCGA +AATTAACTGGAATGCAACACCTTGCACTGGCCGTCCTGCGGTGGTGACCCTTTGAGGTAA +ACACGTCGTCGACGCATTACAGTTGGGAGAAGCACACTCATGTTTCTAATAAAGCGCTCA +CAGACGCGACCACTATAGCTCTAAAATACATCCCTCTAAGGTTCCATCTAGAAAGTGGCC +CCCGCGACCGTCTACCGTGGTGGATGCAGGGAGTCACCTACGCGTCTTTTCGTGCTACCT +AGGCATTTTTGCACTACCTAACTCCGTATTAAGGCCTTCGGAGAGGGCCGTCCCACTTCA +ATGTGTGTGGTGGACTGTCCTCATGGGAAAAGCAAGTGTTTGACCGGTTGACACTAGTCC +CGTTTATCTTCATGGGCGGGAGCGCGCATTCGTGACGGGGACACTTCTCGCCGTTTAGCC +GGTGAGCTTATTAGGCCGATGGCGGGCCACCCTGATACGGGGGCCTATATGTCCACGAAT +ATCAATTTCTGTATAACATTGGGCGCAGAAAACAGACTGGTCCAAATAAGATGAATCTAT +AGCCCAGTGTGTTGCCTAAACGCTGAGCGAATAATTGGTCGCGCTCGGCGAGACCAGGGA diff --git a/pymummer/tests/data/nucmer_test_ref.fa b/pymummer/tests/data/nucmer_test_ref.fa new file mode 100644 index 0000000..0c0c558 --- /dev/null +++ b/pymummer/tests/data/nucmer_test_ref.fa @@ -0,0 +1,18 @@ +>test_ref +TCAAGATCGTGCCCCGTTGATATCGCTGTTGCACAGGACTTTCTCCACCCTGATACCGCA +GTAATCAAATAATCCACCGGATGAGGTATTTTCTCATCGGGGTGACTCTAACCACATCGT +GTTTCTTCCTGAAGGCTCTAAGATGTCATGAGAACTCTTACTGTCTAGCTGAGGGGCTTG +TGCACAACACTAGGATTGTGTCTTATGCTCTATTGGACAGCGAAAACTGCTGAAATTAAC +GGGCCGTAACATACTATATTCTTCAAACCGAATTAACGTTCAGCCCCCGCTTGATTGCGA +AATTAACTGGAATGCAACACCTTGCACTGGCCGTCCTGCGGTGGTGACCCTTTGAGGTAA +ACACGTCGTCGACGCATTACAGTTGGGAGAAGCACACTCATGTTTCTAATAAAGCGCTCA +CAGACGCGACCACTACTACTCTAAAATACATCCCTCTAAGGTTCCATCTAGAAAGTGGCC +CCCGCGACCGTCTACCGTGGTGGATGCAGGGAGTCACCTACGCGTCTTTTCGTGCTACCT +AGGCATTTTTGCACTACCTAACTCCGTATTAAGGCCTTCGGAGAGGGCCGTCCCACTTCA +ATGTGTGTGGTGGACTGTCCTCATGGGAAAAGCAAGTGTTTGACCGGTTGACACTAGTCC +CGTTTATCTTCATGGGCGGGAGCGCGCATTCGTGACGGGGACACTTCTCGCCGTTTAGCC +GGTGAGCTTATTAGGCCGATGGCGGGCCACCCTGATACGGGGGCCTATATGTCCACGAAT +ATCAATTTCTGTATAACATTGGGCGCAGAAAACAGACTGGTCCAAATAAGATGAATCTAT +AGCCCAGTGTGTTGCCTAAACGCTGAGCGAATAATTGGTCGCGCTCGGCGAGACCAGGGA +TTCTGGCAAGATCCTAACTCGGCCGTCAATGATGTTAAATCAACTCGGTGTGGCCCCAGC +TTCGACACCAAAAGTTGTGATCACTACATAGCGTATCTCG diff --git a/pymummer/tests/data/nucmer_test_write_script_no_snps.sh b/pymummer/tests/data/nucmer_test_write_script_no_snps.sh new file mode 100644 index 0000000..a0a09a9 --- /dev/null +++ b/pymummer/tests/data/nucmer_test_write_script_no_snps.sh @@ -0,0 +1,3 @@ +nucmer -p p ref qry +delta-filter p.delta > p.delta.filter +show-coords -dTlro p.delta.filter > outfile diff --git a/pymummer/tests/data/nucmer_test_write_script_with_snps.sh b/pymummer/tests/data/nucmer_test_write_script_with_snps.sh new file mode 100644 index 0000000..d624808 --- /dev/null +++ b/pymummer/tests/data/nucmer_test_write_script_with_snps.sh @@ -0,0 +1,4 @@ +nucmer -p p ref qry +delta-filter p.delta > p.delta.filter +show-coords -dTlro p.delta.filter > outfile +show-snps -TClr p.delta.filter > outfile.snps diff --git a/pymummer/tests/data/snp_file_test_get_all_variants.snps b/pymummer/tests/data/snp_file_test_get_all_variants.snps new file mode 100644 index 0000000..e2a84a6 --- /dev/null +++ b/pymummer/tests/data/snp_file_test_get_all_variants.snps @@ -0,0 +1,8 @@ +125 T . 124 1 124 500 497 1 1 ref1 qry1 +126 A . 124 1 124 500 497 1 1 ref1 qry1 +127 C . 124 1 124 500 497 1 1 ref1 qry1 +386 C T 383 115 115 500 497 1 1 ref1 qry1 +479 . G 480 0 22 500 504 1 1 ref2 qry2 +479 . A 481 0 22 500 504 1 1 ref2 qry2 +479 . T 482 0 22 500 504 1 1 ref2 qry2 +479 . A 483 0 22 500 504 1 1 ref2 qry2 diff --git a/pymummer/tests/data/snp_file_test_no_header.snps b/pymummer/tests/data/snp_file_test_no_header.snps new file mode 100644 index 0000000..833c64f --- /dev/null +++ b/pymummer/tests/data/snp_file_test_no_header.snps @@ -0,0 +1,3 @@ +133 G . 122 1 122 500 489 1 1 ref qry +143 . C 131 1 132 500 489 1 1 ref qry +253 T A 242 120 242 500 489 1 1 ref qry diff --git a/pymummer/tests/data/snp_file_test_with_header.snps b/pymummer/tests/data/snp_file_test_with_header.snps new file mode 100644 index 0000000..ad93e37 --- /dev/null +++ b/pymummer/tests/data/snp_file_test_with_header.snps @@ -0,0 +1,7 @@ +/path/to/ref.fa /path/to/qry.fa +NUCMER + +[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS] +133 G . 122 1 122 500 489 1 1 ref qry +143 . C 131 1 132 500 489 1 1 ref qry +253 T A 242 120 242 500 489 1 1 ref qry diff --git a/pymummer/tests/nucmer_test.py b/pymummer/tests/nucmer_test.py new file mode 100644 index 0000000..787fb28 --- /dev/null +++ b/pymummer/tests/nucmer_test.py @@ -0,0 +1,99 @@ +import unittest +import os +import filecmp +from pymummer import nucmer + +modules_dir = os.path.dirname(os.path.abspath(nucmer.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + + +class TestRunner(unittest.TestCase): + def test_nucmer_command(self): + '''test _nucmer_command''' + tests = [ + [nucmer.Runner('ref', 'qry', 'outfile'), 'nucmer -p pre ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', breaklen=42), 'nucmer -p pre -b 42 ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11), 'nucmer -p pre -D 11 ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', diagdiff=11, promer=True), 'promer -p pre ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', maxmatch=True), 'nucmer -p pre --maxmatch ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', mincluster=42), 'nucmer -p pre -c 42 ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', simplify=False), 'nucmer -p pre --nosimplify ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', promer=True), 'promer -p pre ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', promer=True, breaklen=42), 'promer -p pre -b 42 ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', promer=True, maxmatch=True), 'promer -p pre --maxmatch ref qry'], + [nucmer.Runner('ref', 'qry', 'outfile', promer=True, simplify=False), 'promer -p pre ref qry'] + ] + + for l in tests: + self.assertEqual(l[0]._nucmer_command('ref', 'qry', 'pre'), l[1]) + + + def test_delta_filter_command(self): + '''test _delta_filter_command''' + tests = [ + [nucmer.Runner('ref', 'qry', 'outfile'), 'delta-filter infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile', min_id=42), 'delta-filter -i 42 infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile', min_length=43), 'delta-filter -l 43 infile > outfile'], + ] + + for l in tests: + self.assertEqual(l[0]._delta_filter_command('infile', 'outfile'), l[1]) + + + def test_show_coords_command(self): + '''test _show_coords_command''' + tests = [ + [nucmer.Runner('ref', 'qry', 'outfile', coords_header=False), 'show-coords -dTlro -H infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile'), 'show-coords -dTlro infile > outfile'] + ] + + for l in tests: + self.assertEqual(l[0]._show_coords_command('infile', 'outfile'), l[1]) + + + def test_show_snps_command(self): + '''test _show_snps_command''' + tests = [ + [nucmer.Runner('ref', 'qry', 'outfile', snps_header=False), 'show-snps -TClr -H infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile'), 'show-snps -TClr infile > outfile'], + [nucmer.Runner('ref', 'qry', 'outfile', show_snps_C=False), 'show-snps -Tlr infile > outfile'] + ] + + for nuc_obj, expected in tests: + self.assertEqual(nuc_obj._show_snps_command('infile', 'outfile'), expected) + + + def test_write_script_no_snps(self): + '''test _write_script no snps''' + tmp_script = 'tmp.script.sh' + r = nucmer.Runner('ref', 'qry', 'outfile') + r._write_script(tmp_script, 'ref', 'qry', 'outfile') + expected = os.path.join(data_dir, 'nucmer_test_write_script_no_snps.sh') + self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False)) + os.unlink(tmp_script) + + + def test_write_script_with_snps(self): + '''test _write_script with snps''' + tmp_script = 'tmp.script.sh' + r = nucmer.Runner('ref', 'qry', 'outfile', show_snps='outfile.snps') + r._write_script(tmp_script, 'ref', 'qry', 'outfile') + expected = os.path.join(data_dir, 'nucmer_test_write_script_with_snps.sh') + self.assertTrue(filecmp.cmp(expected, tmp_script, shallow=False)) + os.unlink(tmp_script) + + + def test_run_nucmer(self): + '''test run_nucmer''' + qry = os.path.join(data_dir, 'nucmer_test_qry.fa') + ref = os.path.join(data_dir, 'nucmer_test_ref.fa') + tmp_out = 'tmp.nucmer.out' + runner = nucmer.Runner(ref, qry, tmp_out, coords_header=False, show_snps=True, snps_header=False) + runner.run() + expected = os.path.join(data_dir, 'nucmer_test_out.coords') + self.assertTrue(filecmp.cmp(tmp_out, expected, shallow=False)) + self.assertTrue(filecmp.cmp(tmp_out + '.snps', expected + '.snps', shallow=False)) + os.unlink(tmp_out) + os.unlink(tmp_out + '.snps') + + diff --git a/pymummer/tests/snp_file_test.py b/pymummer/tests/snp_file_test.py new file mode 100644 index 0000000..03a5035 --- /dev/null +++ b/pymummer/tests/snp_file_test.py @@ -0,0 +1,58 @@ +import unittest +import os +from pymummer import snp_file, snp, variant + +modules_dir = os.path.dirname(os.path.abspath(snp_file.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + +class TestUtils(unittest.TestCase): + def test_snp_file(self): + '''test coords_file''' + expected = [ + '\t'.join(['133', 'G', '.', '122', '1', '122', '500', '489', '1', '1', 'ref', 'qry']), + '\t'.join(['143', '.', 'C', '131', '1', '132', '500', '489', '1', '1', 'ref', 'qry']), + '\t'.join(['253', 'T', 'A', '242', '120', '242', '500', '489', '1', '1', 'ref', 'qry']) + ] + + expected = [snp.Snp(x) for x in expected] + + infiles = [os.path.join(data_dir, 'snp_file_test_with_header.snps'), os.path.join(data_dir, 'snp_file_test_no_header.snps')] + + for fname in infiles: + fr = snp_file.reader(fname) + snps = [x for x in fr] + self.assertEqual(snps, expected) + + + def test_get_all_variants(self): + '''Test load all variants from file''' + deletion_snps = [ + '\t'.join(['125', 'T', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), + '\t'.join(['126', 'A', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), + '\t'.join(['127', 'C', '.', '124', '1', '124', '500', '497', '1', '1', 'ref1', 'qry1']), + ] + deletion_snps = [snp.Snp(x) for x in deletion_snps] + deletion_variant = variant.Variant(deletion_snps[0]) + deletion_variant.update_indel(deletion_snps[1]) + deletion_variant.update_indel(deletion_snps[2]) + + just_a_snp = '\t'.join(['386', 'C', 'T', '383', '115', '115', '500', '497', '1', '1', 'ref1', 'qry1']) + snp_variant = variant.Variant(snp.Snp(just_a_snp)) + + insertion_snps = [ + '\t'.join(['479', '.', 'G', '480', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), + '\t'.join(['479', '.', 'A', '481', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), + '\t'.join(['479', '.', 'T', '482', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), + '\t'.join(['479', '.', 'A', '483', '0', '22', '500', '504', '1', '1', 'ref2', 'qry2']), + ] + insertion_snps = [snp.Snp(x) for x in insertion_snps] + insertion_variant = variant.Variant(insertion_snps[0]) + for i in range(1, len(insertion_snps)): + insertion_variant.update_indel(insertion_snps[i]) + + + variants_from_file = snp_file.get_all_variants(os.path.join(data_dir, 'snp_file_test_get_all_variants.snps')) + self.assertEqual(len(variants_from_file), 3) + self.assertEqual(variants_from_file[0], deletion_variant) + self.assertEqual(variants_from_file[1], snp_variant) + self.assertEqual(variants_from_file[2], insertion_variant) diff --git a/pymummer/tests/snp_test.py b/pymummer/tests/snp_test.py new file mode 100644 index 0000000..ddc07cf --- /dev/null +++ b/pymummer/tests/snp_test.py @@ -0,0 +1,24 @@ +import unittest +import os +from pymummer import snp + + +modules_dir = os.path.dirname(os.path.abspath(snp.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + + +class TestSnp(unittest.TestCase): + def test_str_no_c_option(self): + '''Test __str__ with format with no -C option''' + l_in = ['187', 'A', 'C', '269', '187', '187', '654', '853', '1', '1', 'ref_name', 'qry_name'] + s = snp.Snp('\t'.join(l_in)) + expected = '\t'.join(['187', 'A', 'C', '269', '654', '853', '1', 'ref_name', 'qry_name']) + self.assertEqual(str(s), expected) + + + def test_str_with_c_option(self): + '''Test __str__ with format with -C option''' + l_in = ['187', 'A', 'C', '269', '187', '187', '0', '0', '654', '853', '1', '-1', 'ref_name', 'qry_name'] + s = snp.Snp('\t'.join(l_in)) + expected = '\t'.join(['187', 'A', 'C', '269', '654', '853', '-1', 'ref_name', 'qry_name']) + self.assertEqual(str(s), expected) diff --git a/pymummer/tests/syscall_test.py b/pymummer/tests/syscall_test.py new file mode 100644 index 0000000..586fa70 --- /dev/null +++ b/pymummer/tests/syscall_test.py @@ -0,0 +1,16 @@ +import unittest +import os +from pymummer import syscall + + +class TestSyscall(unittest.TestCase): + def test_run_fail(self): + '''Test that run raises error when command fails''' + with self.assertRaises(syscall.Error): + syscall.run('notacommandandthrowerror') + + + def test_run_ok(self): + '''Test run is ok on command that works''' + syscall.run('ls') + diff --git a/pymummer/tests/variant_test.py b/pymummer/tests/variant_test.py new file mode 100644 index 0000000..300d9e6 --- /dev/null +++ b/pymummer/tests/variant_test.py @@ -0,0 +1,103 @@ +import unittest +import copy +import os +from pymummer import variant, snp + +modules_dir = os.path.dirname(os.path.abspath(variant.__file__)) +data_dir = os.path.join(modules_dir, 'tests', 'data') + + +class TestVariant(unittest.TestCase): + def test_init(self): + '''Test init gets correct variant type''' + lines = [ + ['42', 'T', 'A', '42', '42', '42', '1000', '1000', '1', '1', 'ref', 'ref'], + ['242', 'G', '.', '241', '1', '241', '1000', '1000', '1', '1', 'ref', 'ref'], + ['300', '.', 'G', '298', '0', '298', '1000', '1000', '1', '1', 'ref', 'ref'] + ] + + variants = [variant.Variant(snp.Snp('\t'.join(x))) for x in lines] + expected = [variant.SNP, variant.DEL, variant.INS] + for i in range(len(lines)): + self.assertEqual(variants[i].var_type, expected[i]) + + + def test_update_indel_no_change(self): + '''Test update_indel does nothing in the right cases''' + initial_vars = [ + snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + ] + + to_add = [ + snp.Snp('\t'.join(['142', 'A', '.', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['142', '.', 'A', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])), + snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])), + snp.Snp('\t'.join(['44', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])), + snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])), + snp.Snp('\t'.join(['44', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])), + ] + + assert len(initial_vars) == len(to_add) + + for i in range(len(initial_vars)): + var = variant.Variant(initial_vars[i]) + var_original = copy.copy(var) + self.assertFalse(var.update_indel(to_add[i])) + self.assertEqual(var, var_original) + + def test_update_indel_insertion(self): + '''Test update_indel extends insertions correctly''' + insertion = variant.Variant(snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry']))) + to_add = snp.Snp('\t'.join(['42', '.', 'C', '101', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry'])) + expected = copy.copy(insertion) + # coords stored zero-based, so subtract 1 from the real expected coords + expected.ref_start = 41 + expected.ref_end = 41 + expected.ref_length = 300 + expected.ref_name = 'ref' + expected.ref_base = '.' + expected.qry_start = 99 + expected.qry_end = 100 + expected.qry_length = 400 + expected.qry_name = 'qry' + expected.qry_base = 'AC' + self.assertTrue(insertion.update_indel(to_add)) + self.assertEqual(expected, insertion) + + + def test_update_indel_deletion(self): + '''Test update_indel extends deletions correctly''' + deletion = variant.Variant(snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry']))) + to_add = snp.Snp('\t'.join(['43', 'C', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])) + expected = copy.copy(deletion) + # coords stored zero-based, so subtract 1 from the real expected coords + expected.ref_start = 41 + expected.ref_end = 42 + expected.ref_length = 300 + expected.ref_name = 'ref' + expected.ref_base = 'AC' + expected.qry_start = 99 + expected.qry_end = 99 + expected.qry_length = 400 + expected.qry_name = 'qry' + expected.qry_base = '.' + self.assertTrue(deletion.update_indel(to_add)) + self.assertEqual(expected, deletion) + diff --git a/pymummer/variant.py b/pymummer/variant.py new file mode 100644 index 0000000..457a035 --- /dev/null +++ b/pymummer/variant.py @@ -0,0 +1,85 @@ +class Error (Exception): pass + +SNP = 1 +DEL = 2 +INS = 3 + +var_types = { + 1: 'SNP', + 2: 'DEL', + 3: 'INS', +} + + +class Variant: + def __init__(self, snp): + '''Create a Variant object from a pymummer.snp.Snp object''' + if snp.ref_base == '.': + self.var_type = INS + self.qry_base = snp.qry_base + self.ref_base = '.' + elif snp.qry_base == '.': + self.var_type = DEL + self.qry_base = '.' + self.ref_base = snp.ref_base + elif '.' not in [snp.ref_base, snp.qry_base]: + self.var_type = SNP + self.ref_base = snp.ref_base + self.qry_base = snp.qry_base + else: + raise Error('Error constructing Variant from pymummer.snp.Snp:' + str(snp)) + + self.ref_start = snp.ref_pos + self.ref_end = snp.ref_pos + self.ref_length = snp.ref_length + self.ref_name = snp.ref_name + self.qry_start = snp.qry_pos + self.qry_end = snp.qry_pos + self.qry_length = snp.qry_length + self.qry_name = snp.qry_name + self.reverse = snp.reverse + + + def __eq__(self, other): + return type(other) is type(self) and self.__dict__ == other.__dict__ + + + def __str__(self): + return '\t'.join([ + str(self.ref_start + 1), + str(self.ref_end + 1), + str(self.ref_length), + str(self.ref_name), + self.ref_base, + str(self.qry_start + 1), + str(self.qry_end + 1), + str(self.qry_length), + str(self.qry_name), + self.qry_base, + '-1' if self.reverse else '1', + ]) + + def update_indel(self, nucmer_snp): + '''Indels are reported over multiple lines, 1 base insertion or deletion per line. This method extends the current variant by 1 base if it's an indel and adjacent to the new SNP and returns True. If the current variant is a SNP, does nothing and returns False''' + new_variant = Variant(nucmer_snp) + if self.var_type not in [INS, DEL] \ + or self.var_type != new_variant.var_type \ + or self.qry_name != new_variant.qry_name \ + or self.ref_name != new_variant.ref_name \ + or self.reverse != new_variant.reverse: + return False + if self.var_type == INS \ + and self.ref_start == new_variant.ref_start \ + and self.qry_end + 1 == new_variant.qry_start: + self.qry_base += new_variant.qry_base + self.qry_end += 1 + return True + if self.var_type == DEL \ + and self.qry_start == new_variant.qry_start \ + and self.ref_end + 1 == new_variant.ref_start: + self.ref_base += new_variant.ref_base + self.ref_end += 1 + return True + + return False + diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..453b68c --- /dev/null +++ b/setup.py @@ -0,0 +1,45 @@ +import os +import glob +import shutil +import sys +from setuptools import setup, find_packages + + +required_progs = ['nucmer', 'show-coords', 'show-snps', 'delta-filter'] +found_all_progs = True +print('Checking MUMmer programs found in path:') + +for program in required_progs: + if shutil.which(program) is None: + found_all_progs = False + found = ' NOT FOUND' + else: + found = ' OK' + + print(found, program, sep='\t') + + +if not found_all_progs: + print('Cannot install because some programs from the MUMer package not found.', file=sys.stderr) + sys.exit(1) + + +setup( + name='pymummer', + version='0.11.0', + description='Wrapper for MUMmer', + packages = find_packages(), + author='Martin Hunt, Nishadi De Silva', + author_email='path-help@sanger.ac.uk', + url='https://github.com/sanger-pathogens/pymummer', + test_suite='nose.collector', + install_requires=['pyfastaq >= 3.10.0'], + tests_require=['nose >= 1.3'], + license='GPLv3', + classifiers=[ + 'Development Status :: 4 - Beta', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Programming Language :: Python :: 3 :: Only', + 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', + ], +) -- cgit v1.2.3 From bc956bca6a1e11ab5598994956a13fb0829bbeb1 Mon Sep 17 00:00:00 2001 From: Nilesh Patra Date: Fri, 28 Aug 2020 16:58:54 +0200 Subject: Import python-pymummer_0.11.0-2.debian.tar.xz [dgit import tarball python-pymummer 0.11.0-2 python-pymummer_0.11.0-2.debian.tar.xz] --- changelog | 93 +++++++++++++++++++++++++++++++++++++++++++++++++++++ control | 29 +++++++++++++++++ copyright | 29 +++++++++++++++++ docs | 1 + rules | 21 ++++++++++++ salsa-ci.yml | 4 +++ source/format | 1 + tests/control | 3 ++ tests/run-unit-test | 8 +++++ upstream/metadata | 9 ++++++ watch | 4 +++ 11 files changed, 202 insertions(+) create mode 100644 changelog create mode 100644 control create mode 100644 copyright create mode 100644 docs create mode 100755 rules create mode 100644 salsa-ci.yml create mode 100644 source/format create mode 100644 tests/control create mode 100644 tests/run-unit-test create mode 100644 upstream/metadata create mode 100644 watch diff --git a/changelog b/changelog new file mode 100644 index 0000000..18d63d5 --- /dev/null +++ b/changelog @@ -0,0 +1,93 @@ +python-pymummer (0.11.0-2) unstable; urgency=medium + + * Team Upload. + * Add autopkgtests + + -- Nilesh Patra Fri, 28 Aug 2020 20:28:54 +0530 + +python-pymummer (0.11.0-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. (routine-update) + * lintian complained about missing maintainer, added Andreas and myself + * removed egg.info files + + -- Steffen Moeller Wed, 10 Jun 2020 02:13:58 +0200 + +python-pymummer (0.10.3-2) unstable; urgency=medium + + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.3.0 + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target + + -- Andreas Tille Mon, 07 Jan 2019 09:37:20 +0100 + +python-pymummer (0.10.3-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Sascha Steinbiss Mon, 29 Jan 2018 15:46:12 +0100 + +python-pymummer (0.10.2-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Sascha Steinbiss Thu, 02 Feb 2017 14:30:00 +0100 + +python-pymummer (0.10.1-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Sascha Steinbiss Fri, 18 Nov 2016 19:58:54 +0000 + +python-pymummer (0.10.0-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Sascha Steinbiss Tue, 15 Nov 2016 11:18:13 +0000 + +python-pymummer (0.9.0-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Sascha Steinbiss Tue, 18 Oct 2016 18:37:05 +0000 + +python-pymummer (0.8.1-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + * Bump Standards-Version. + + -- Sascha Steinbiss Wed, 24 Aug 2016 13:45:50 +0000 + +python-pymummer (0.7.1-1) unstable; urgency=low + + * Update Standards-Version + * Imported Upstream version 0.7.1 + + -- Afif Elghraoui Sat, 23 Apr 2016 20:25:13 -0700 + +python-pymummer (0.7.0-1) unstable; urgency=medium + + * Imported Upstream version 0.7.0 + * Use secure VCS URLs + * Bump copyright year + + -- Afif Elghraoui Fri, 12 Feb 2016 01:09:47 -0800 + +python-pymummer (0.6.1-1) unstable; urgency=low + + * Initial release (Closes: #805230) + + -- Afif Elghraoui Sun, 15 Nov 2015 15:00:31 -0800 diff --git a/control b/control new file mode 100644 index 0000000..a6f2d7f --- /dev/null +++ b/control @@ -0,0 +1,29 @@ +Source: python-pymummer +Maintainer: Debian Med Packaging Team +Uploaders: Steffen Moeller , + Andreas Tille +Section: python +Testsuite: autopkgtest-pkg-python +Priority: optional +Build-Depends: debhelper-compat (= 13), + dh-python, + python3-all, + python3-setuptools, + fastaq (>=3.10.0), + mummer, + python3-nose +Standards-Version: 4.5.0 +Vcs-Browser: https://salsa.debian.org/med-team/python-pymummer +Vcs-Git: https://salsa.debian.org/med-team/python-pymummer.git +Homepage: https://github.com/sanger-pathogens/pymummer +Rules-Requires-Root: no + +Package: python3-pymummer +Architecture: all +Depends: ${misc:Depends}, + ${python3:Depends}, + fastaq (>=3.10.0), + mummer +Description: Python 3 interface to MUMmer + pymummer is a Python wrapper for running the programs of the MUMmer + sequence alignment suite and parsing their output. diff --git a/copyright b/copyright new file mode 100644 index 0000000..450527f --- /dev/null +++ b/copyright @@ -0,0 +1,29 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: pymummer +Upstream-Contact: Martin Hunt +Source: https://github.com/sanger-pathogens/pymummer + +Files: * +Copyright: 2015-2016 Martin Hunt + Nishadi De Silva +License: GPL-3.0 + +Files: debian/* +Copyright: 2015-2016 Afif Elghraoui +License: GPL-3.0 + +License: GPL-3.0 + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see . + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". diff --git a/docs b/docs new file mode 100644 index 0000000..b43bf86 --- /dev/null +++ b/docs @@ -0,0 +1 @@ +README.md diff --git a/rules b/rules new file mode 100755 index 0000000..e19ff93 --- /dev/null +++ b/rules @@ -0,0 +1,21 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 + +include /usr/share/dpkg/default.mk + +export PYBUILD_NAME=pymummer + +%: + LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild + +override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + PYBUILD_SYSTEM=custom \ + PYBUILD_TEST_ARGS="{interpreter} setup.py test" \ + dh_auto_test +endif + +override_dh_auto_clean: + rm -f pymummer.egg-info/PKG-INFO pymummer.egg-info/SOURCES.txt pymummer.egg-info/dependency_links.txt pymummer.egg-info/requires.txt pymummer.egg-info/top_level.txt + rm -rf .pybuild pymummer/tests/__pycache__ pymummer/__pycache__ diff --git a/salsa-ci.yml b/salsa-ci.yml new file mode 100644 index 0000000..33c3a64 --- /dev/null +++ b/salsa-ci.yml @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..4b450a8 --- /dev/null +++ b/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, python3-all, python3-pytest +Restrictions: allow-stderr diff --git a/tests/run-unit-test b/tests/run-unit-test new file mode 100644 index 0000000..0b19e00 --- /dev/null +++ b/tests/run-unit-test @@ -0,0 +1,8 @@ +#!/bin/bash +set -e + +for py in $(py3versions -r 2> /dev/null) +do + $py -m pytest -v +done + diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 index 0000000..8f4c0dc --- /dev/null +++ b/upstream/metadata @@ -0,0 +1,9 @@ +Bug-Database: https://github.com/sanger-pathogens/pymummer/issues +Bug-Submit: https://github.com/sanger-pathogens/pymummer/issues/new +Registry: + - Name: conda:bioconda + Entry: pymummer + - Name: OMICtools + Entry: NA +Repository: https://github.com/sanger-pathogens/pymummer.git +Repository-Browse: https://github.com/sanger-pathogens/pymummer diff --git a/watch b/watch new file mode 100644 index 0000000..a586a89 --- /dev/null +++ b/watch @@ -0,0 +1,4 @@ +version=3 + +opts="filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/python-pymummer-$1.tar.gz/" \ + https://github.com/sanger-pathogens/pymummer/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz -- cgit v1.2.3