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        "author": "Shaurita Hutchins & Robert Gilmore",
        "author_email": "datasnakes@gmail.com",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.5",
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        "description": "[![Build Status](https://travis-ci.org/datasnakes/htseq-count-cluster.svg?branch=master)](https://travis-ci.org/datasnakes/htseq-count-cluster)\n\n# htseq-count-cluster\n\nA cli wrapper for running [htseq](https://github.com/simon-anders/htseq)'s `htseq-count` on a cluster.\n\nView [documentation](https://tinyurl.com/yb7kz7zz).\n\n## Install\n\n`pip install HTSeqCountCluster`\n\n## Features\n\n- For use with large datasets (we've previously used a dataset of 120 different human samples)\n- For use with SGE/SGI cluster systems\n- Submits multiple jobs\n- Command line interface/script\n- Merges counts files into one counts table/csv file\n- Uses `accepted_hits.bam` file output of `tophat`\n\n### Examples\n\n#### Run htseq-count-cluster\n\nAfter generating bam output files from tophat, instead of using HTSeq's htseq count, you\ncan use our `htseq-count-cluster` script. This script is intended for use with\nclusters that are using pbs (qsub) for job monitoring.\n\n```bash\nhtseq-count-cluster -p path/to/bam-files/ -f samples.csv -g genes.gtf -o path/to/cluster-output/\n```\n\n| Argument |                                                                             Description                                                                             | Required |\n|:--------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:--------:|\n|   `-p`   | This is the path of your .bam files.  Presently, this script looks for a folder that is the sample name and searches for an accepted_hits.bam file (tophat output). |    Yes   |\n|   `-i`   |                                                     You should have a csv file list of your samples or folder names (no header).                                                    |    Yes   |\n|   `-g`   |                                                           This should be the path to your genes.gtf file.                                                           |    Yes   |\n|   `-o`   |                                                  This should be an existing directory for your output counts files.                                                 |    Yes   |\n|   `-e`   |\n\nThis script uses logzero so there will be color coded logging information to your shell.\n\nA common linux practice is to use `screen` to create a new shell and run a program\nso that if it does produce output to the stdout/shell, the user can exit that particular\nshell without the program ending and utilize another shell.\n\n##### Help message output for `htseq-count-cluster`\n\n```\nusage: htseq-count-cluster [-h] -p INPATH -f INFILE -g GTF -o OUTPATH\n                              [-e EMAIL]\n\nThis is a command line wrapper around htseq-count.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -p INPATH, --inpath INPATH\n                        Path of your samples/sample folders.\n  -f INFILE, --infile INFILE\n                        Name or path to your input csv file.\n  -g GTF, --gtf GTF     Name or path to your gtf/gff file.\n  -o OUTPATH, --outpath OUTPATH\n                        Directory of your output counts file. The counts file\n                        will be named.\n  -e EMAIL, --email EMAIL\n                        Email address to send script completion to.\n\n*Ensure that htseq-count is in your path.\n\n\n```\n\n\n#### Merge output counts files\n\nIn order to prep your data for `DESeq2`, `limma` or `edgeR`, it's best to have 1 merged\ncounts file instead of multiple files produced from the `htseq-count-cluster` script. We offer this\nas a standalone script as it may be useful to keep those files separate.\n\n```bash\nmerge-counts -d path/to/cluster-output/\n```\n\n##### Help message for `merge-counts`\n\n```\nusage: merge-counts [-h] -d DIRECTORY\n\nMerge multiple counts tables into 1 counts .csv file.\n\nYour output file will be named:  merged_counts_table.csv\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -d DIRECTORY, --directory DIRECTORY\n                        Path to folder of counts files.\n```\n\n## ToDo\n\n- [ ] Monitor jobs.\n- [ ] Enhance wrapper input for other use cases.\n- [ ] Add example data.\n\n\n## Maintainers\n\nShaurita Hutchins | [@sdhutchins](https://github.com/sdhutchins) | [\u2709](mailto:sdhutchins@outlook.com)\nRob Gilmore | [@grabear](https://github.com/grabear) | [\u2709](mailto:robgilmore127@gmail.com)\n\n\n## Help\n\nPlease feel free to [open an issue](https://github.com/datasnakes/htseq-count-cluster/issues/new) if you have a question/feedback/problem\nor [submit a pull request](https://github.com/datasnakes/htseq-count-cluster/compare) to add a feature/refactor/etc. to this project.\n\n\n",
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        "keywords": "science lab pyschiatry rnaseq htseq",
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