{"id":16636882,"url":"https://github.com/widdowquinn/thapbi-pycits","last_synced_at":"2026-03-15T12:06:32.912Z","repository":{"id":144924666,"uuid":"71804478","full_name":"widdowquinn/THAPBI-pycits","owner":"widdowquinn","description":"Repository for ITS diagnostics development as part of Phytothreats project","archived":false,"fork":false,"pushed_at":"2017-12-20T14:29:33.000Z","size":8572,"stargazers_count":1,"open_issues_count":4,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-18T11:35:06.292Z","etag":null,"topics":["bioinformatics","classification","computational-biology","its1","metabarcoding"],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/widdowquinn.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-10-24T15:43:11.000Z","updated_at":"2019-06-18T13:02:25.000Z","dependencies_parsed_at":"2023-07-22T00:20:06.770Z","dependency_job_id":null,"html_url":"https://github.com/widdowquinn/THAPBI-pycits","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/widdowquinn%2FTHAPBI-pycits","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/widdowquinn%2FTHAPBI-pycits/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/widdowquinn%2FTHAPBI-pycits/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/widdowquinn%2FTHAPBI-pycits/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/widdowquinn","download_url":"https://codeload.github.com/widdowquinn/THAPBI-pycits/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243141256,"owners_count":20242817,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","classification","computational-biology","its1","metabarcoding"],"created_at":"2024-10-12T06:23:14.819Z","updated_at":"2025-12-24T12:13:28.932Z","avatar_url":"https://github.com/widdowquinn.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![THAPBI-pycits TravisCI build status](https://api.travis-ci.org/widdowquinn/THAPBI-pycits.svg?branch=master)](https://travis-ci.org/widdowquinn/THAPBI-pycits/branches)\n[![codecov.io coverage status](https://img.shields.io/codecov/c/github/widdowquinn/THAPBI-pycits.svg)](https://codecov.io/gh/widdowquinn/THAPBI-pycits)\n[![Code Health](https://landscape.io/github/widdowquinn/THAPBI-pycits/master/landscape.svg?style=flat)](https://landscape.io/github/widdowquinn/THAPBI-pycits/master)\n\n* [Travis-CI page](https://travis-ci.org/widdowquinn/THAPBI-pycits/branches)\n* [`codecov.io` page](https://codecov.io/gh/widdowquinn/THAPBI-pycits)\n* [`landscape.io` page](https://landscape.io/github/widdowquinn/THAPBI-pycits/1)\n\n# README.py - `THAPBI-pycits`\nThis repository is for development of ITS1-based diagnostic/profiling tools for the THAPBI Phyto-Threats project, funded by BBSRC.\n\n# DEVELOPER NOTES\n\n## Python style conventions\n\nIn this repository, we're trying to keep to the Python [PEP8 style convention](https://www.python.org/dev/peps/pep-0008/), the [PEP257 docstring conventions](https://www.python.org/dev/peps/pep-0257/), and the [Zen of Python](https://www.python.org/dev/peps/pep-0020/). To help in this, a pre-commit hook script is provided in the `git_hooks` subdirectory that, if deployed in the `Git` repository, checks Python code for PEP8 correctness before permitting a `git commit` command to go to completion.\n\nIf the `pep8` module is not already present, it can be installed using `pip install pep8`\n\nWhether you choose to use this or not, the `THAPBI-pycits` repository is registered with `landscape.io`, and the \"health\" of the code is assessed and reported for every repository push.\n\n* [`landscape.io` page](https://landscape.io/github/widdowquinn/THAPBI-pycits)\n\n### Installing the `git hook`\n\nTo install the pre-commit hook:\n\n1. clone the repository with `git clone https://github.com/widdowquinn/THAPBI` (you may already have done this)\n2. change directory to the root of the repository with `cd THAPBI-pycits`\n3. copy the pre-commit script to the `.git/hooks` directory with `cp git_hooks/pre-commit .git/hooks/`\n\n## Using a virtual environment with the repository\n\nIn the root directory of the repository:\n\n```\n$ virtualenv -p python3.5 venv-THAPBI-pycits\n$ source venv-THAPBI-pycits/bin/activate\n\u003cactivity\u003e\n$ deactivate\n```\n\n# INSTALLATION\n\n## Dependencies: Python modules\n\nAll Python module dependencies are described in `requirements.txt` and can be installed using\n\n```\npip install -r requirements.txt\n```\n\nThere may be issues with `biom-format` and `biopython` installations due to ordering of module installation. If this is the case for you, then it might be solved by installing `numpy` at the command-line first, with:\n\n```\npip install numpy\npip install -r requirements.txt\n```\n\n## Dependencies: Third-party applications\n\n\n### `pear`\n\n* [home page](http://sco.h-its.org/exelixis/web/software/pear/)\n\n`pear` is a paired-end read merger, used by the pipeline to merge ITS paired-end reads into a single ITS sequence. It is available from the [`pear` home page](http://sco.h-its.org/exelixis/web/software/pear/) as a precompiled executable that can be placed in your `$PATH`, and it can be installed on the Mac with [Homebrew](http://brew.sh/) and [homebrew-science](https://github.com/Homebrew/homebrew-science), using:\nIf you are having trouble on some Linux system due to bzip+zlib issues, a precompiled version is availble: https://github.com/xflouris/PEAR/blob/master/bin/pear-0.9.5-bin-64\n```\nbrew install pear\n```\nplease rename the binary to pear:\n```\nwget http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.10-bin-64.tar.gz\ntar -zxvf pear-0.9.10-bin-64.tar.gz\ncp pear-0.9.10-bin-64/pear-0.9.10-bin-64 pear-0.9.10-bin-64/pear\nput this in your PATH\n```\n\n### `Trimmomatic`\n\n* [home page](http://www.usadellab.org/cms/?page=trimmomatic)\n\n`Trimmomatic` is used to trim and quality-control the input reads. `pycits` expects `Trimmomatic` to be available at the command-line as `trimmomatic`. You can check if the tool is installed this way with the command:\n\n```\nwhich trimmomatic\n```\n\nTo obtain `Trimmomatic` with this installation type on Linux systems, you can use:\n\n```\napt-get install trimmomatic\n```\n\nand on the Mac (with [Homebrew](http://brew.sh/) and [homebrew-science](https://github.com/Homebrew/homebrew-science)):\n\n```\nbrew install trimmomatic\n```\n\nIf you have downloaded the Java `.jar.` file from [`trimmomatic`'s home page](http://www.usadellab.org/cms/?page=trimmomatic), you can wrap the `.jar` file with a Bash script called `trimmomatic` in your `$PATH`, such as\n\n```\n#!/bin/bash\nexec java -jar $TRIMMOMATIC \"$@\"\n```\n\nwhere `$TRIMMOMATIC` is the path to your `trimmomatic .jar` file.\n\n\n### `muscle`\n\n* [home page](http://www.drive5.com/muscle/muscle.html)\n\n`muscle` MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences [`muscle` download page]http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz as a precompiled executable that can be placed in your `$PATH` when decompressed. Please rename to muscle\n\n```\nwget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz\ntar -zxvf muscle3.8.31_i86linux32.tar.gz\ncp muscle3.8.31_i86linux32 muscle\nput this in your PATH\n```\n\n\n### `fastqc`\n\n* [home page](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n\n`fastqc` fastqc A quality control tool for high throughput sequence data. [`fastqc` download page]http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz as a precompiled executable that can be placed in your `$PATH` when decompressed.\n\n```\nwget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip\nunzip fastqc_v0.11.5.zip\ncd FastQC\nchmod 755 fastqc\nput this in your PATH\n```\n\n### `spades`\n\n* [home page](http://bioinf.spbau.ru/spades)\n\n`spades` spades is an assembly program which we use for error correction. [`spades` download page]http://spades.bioinf.spbau.ru/release3.9.1/SPAdes-3.9.1-Linux.tar.gz as a precompiled executable that can be placed in your `$PATH` when decompressed.\n\n```\nwget http://spades.bioinf.spbau.ru/release3.9.1/SPAdes-3.9.1-Linux.tar.gz\ntar -zxvf SPAdes-3.9.1-Linux.tar.gz\ncd ./SPAdes-3.9.1-Linux/bin/\nput this in your PATH\n```\n\n### `flash`\n\n* [home page](https://ccb.jhu.edu/software/FLASH/)\n\n`flash` flash is a pair end read assembly program. [`flash` download page]https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz as a precompiled executable that can be placed in your `$PATH` when decompressed.\n\n```\nwget https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz\ntar -zxvf FLASH-1.2.11.tar.gz\ncd FLASH-1.2.11\nput this in your PATH\n```\n\n### `swarm`\n\n* [home page](https://ccb.jhu.edu/software/FLASH/)\n\n`swarm` swarm is a clustering program. [`swarm` download page]https://github.com/torognes/swarm \n\n```\ngit clone https://github.com/torognes/swarm.git\ncd swarm/src\nmake\nput PATH_TO/swarm/bin in your PATH\n```\n\n### `blastclust`\n\n* [home page](https://ccb.jhu.edu/software/FLASH/)\n\n`blastclust` blastclust is a clustering program. This is not essential to download. [`blastclust` download page]ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz as a precompiled executable that can be placed in your `$PATH` when decompressed.\n\n```\nwget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz\ntar -zxvf blast-2.2.26-x64-linux.tar.gz\nput this in your PATH\n```\n  \n### `cd-hit`\n\n* [home page](https://github.com/weizhongli/cdhit)\n\n`cd-hit` cd-hit is a clustering program. [`cd-hit` download page]https://github.com/weizhongli/cdhit\n\n```\ngit clone git@github.com:weizhongli/cdhit.git\ncd cdhit\nmake\nput PATH_TO/cdhit in your PATH\n```\n\n### `bowtie_2.2.5`\n\n* [home page](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)\n\n`bowtie_2.2.5` bowtie_2.2.5 is a read mapping program. [`bowtie_2.2.5` download page]https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz\nWe have use the pre compiled binary to reduce difficulty in getting this to work.\n\n```\nmkdir bowtie_2.2.5\ncd bowtie_2.2.5\nwget https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz\ntar -zxvf bowtie2-2.2.5-Linux-x86_64.tar.gz\nput this in your path\nexport PATH=$HOME/bowtie_2.2.5/bin/:$PATH\n```\n\n### `samtools_1.2`\n\n* [home page](http://www.htslib.org/doc/samtools.html)\n\n`samtools_1.2` samtools_1.2 is a program to do lots of thing with sam/ bam files. [`samtools_1.2` download page]https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz\nWe have use the pre compiled binary to reduce difficulty in getting this to work.\n\n```\nmkdir samtools_1.2\ncd samtools_1.2\nwget https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz\ntar -zxvf samtools-1.2-Linux-x86_64.tgz\nput this in your path\nexport PATH=$HOME/samtools_1.2/bin/:$PATH\n```\n\n### `vsearch`\n\n* [home page](https://github.com/torognes/vsearch)\n\n`vsearch` vsearch Versatile open-source tool for metagenomics. [`vsearch` download page]https://github.com/torognes/vsearch\n\n```\nwget https://github.com/torognes/vsearch/releases/download/v2.4.0/vsearch-2.4.0-linux-x86_64.tar.gz\ntar xzf vsearch-2.4.0-linux-x86_64.tar.gz\n```\n\n\n### More information\n\n* Git hooks (`git`): [https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks)\n* Git hooks (tutorial): [http://githooks.com/](http://githooks.com/)\n* PEP8: [https://www.python.org/dev/peps/pep-0008/](https://www.python.org/dev/peps/pep-0008/)\n* PEP257: [https://www.python.org/dev/peps/pep-0257/](https://www.python.org/dev/peps/pep-0257/)\n* Zen of Python (PEP20): [https://www.python.org/dev/peps/pep-0020/](https://www.python.org/dev/peps/pep-0020/)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwiddowquinn%2Fthapbi-pycits","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwiddowquinn%2Fthapbi-pycits","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwiddowquinn%2Fthapbi-pycits/lists"}