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        "author": "Pierre-Edouard GUERIN",
        "author_email": "pierre-edouard.guerin@cefe.cnrs.fr",
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            "Programming Language :: Python :: 3"
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        "description": "`demort` evaluates demultiplexed fastq files by computing various metrics.\n\n# DEPENDENCIES\n\nYou need to install [python 3.7](https://www.python.org/download/releases/3.0/) and depencies. Check version by typing on:\n```\npython3 --version\n```\n**python3 depencies :**\n* [joblib](https://joblib.readthedocs.io/en/latest/installing.html)\n* [biopython](https://github.com/biopython/biopython)\n* [matplotlib](https://matplotlib.org/3.1.1/faq/installing_faq.html)\n\n\n# USAGE\n\n`demort` check fastq files into specified folder(s) then count number of reads for each fastq files for each folder and finally return a summary `csv` table and a `pdf` boxplot picture.\n\n(process a list of folder as a strings)\n```\ndemort.py -d folder/folder1,folder/folder2,folder/folder3 \\\n -t 8 \\\n -p results.pdf \\\n -o results.csv\n```\n(process a list of folder into a file)\n```\ndemort.py -d example/folder_to_process.txt \\\n -t 8 \\\n -p results.pdf \\\n -o results.csv\n```\n\n# COMMAND-LINE ARGUMENTS\n\n| complete flag argument | short flag |Default value | Summary |\n| --- | --- | --- | --- |\n| `--inputFolder` | `-d` | NA |  a string of folderpath separated by coma `,` OR a file containing a list |\n| `--threads` | `-t` | 1 | Number of available cores |\n| `--output_pdf` | `-p` | NA | path of the file where to write a `pdf` boxplot picture |\n| `--output_csv` | `-o` | NA | path of the file where to write a `csv` table |\n\n\n# INPUT\n\n```\nfolder/\n\u251c\u2500\u2500 folder1\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 fqfileA.fq.gz\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 fqfileB.fq.gz\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 fqfileC.fq.gz\n\u251c\u2500\u2500 folder2\n\u2502\u00a0\u00a0 \u251c\u2500\u2500 fqfileD.fq.gz\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 fqfileE.fq.gz\n\u2514\u2500\u2500 folder3\n    \u251c\u2500\u2500 fqfileF.fq.gz\n    \u251c\u2500\u2500 fqfileG.fq.gz\n    \u2514\u2500\u2500 fqfileH.fq.gz\n```\n\n# OUTPUTS\n\n* summary `csv` table [foldername, filename, number of reads]\n* `pdf` boxplot picture\n\n# SYSTEM REQUIREMENTS\n\nLinux (64-bit and 32-bit with slightly limited functionality) and macOS (OS X) are supported.\n\n\n",
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