{ "info": { "author": "Adam Labadorf", "author_email": "labadorf@bu.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: OS Independent", "Operating System :: POSIX", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules", "Topic :: Utilities" ], "description": "# Welcome to fastqcparser\n\npython API for parsing the output of `FastQC `.\n\n# Installation\n\n1. Recomended way to install is using ``pip``\n\n```\npip install fastqcparser\n```\n\n2. Alternatively you can install with ``easy_install``\n::\n\n```\neasy_install fastqcparser\n```\n\n3. You can also install from Github source code.\n::\n\n```\ncd\ngit clone http://bitbucket.org/bubioinformaticshub/fastqcparser.git\ncd fastqcparser\npython setup.py install\n```\n\n# Usage/lazy documentation\n\n```python\n\n# import fastqcparser\nfrom pprint import pprint\nfrom fastqcparser import FastQCParser\n\n# load file\nf = FastQCParser('/path/to/fastqc_output_file.txt')\n\n# or\nf = FastQCParser('/path/to/fastqc.zip')\n\n# or\nwith open('/path/to/fastqc_data.txt') as fp :\n f = FastQCParser(fp)\n\n# or\nwith FastQCParser('/path/to/fastqc_output_file.txt') as f :\n print(f)\n\n# some convenience fields are available from the Basic Statistics module\nprint('\\n'.join([\n f.filename,\n f.file_type,\n f.encoding,\n f.total_sequences,\n f.filtered_sequences,\n f.sequence_length,\n f.percent_gc\n]))\n\n# the available modules are in f.modules\npprint(list(f.modules.keys()))\n\n#['Basic Statistics',\n# 'Per base sequence quality',\n# 'Per sequence quality scores',\n# 'Per base sequence content',\n# 'Per base GC content',\n# 'Per sequence GC content',\n# 'Per base N content',\n# 'Sequence Length Distribution',\n# 'Sequence Duplication Levels',\n# 'Overrepresented sequences',\n# 'Kmer Content']\n\n# you can access an individual module either as a key of f.modules or using\n# f itself:\npprint(f.modules['Basic Statistics'])\npprint(f['Basic Statistics'])\n\n# each module contains a dictionary\npprint(f['Basic Statistics'])\n\n#{'addnl': {},\n# 'data': [['Filename', 'sample1.fastq'],\n# ['File type', 'Conventional base calls'],\n# ['Encoding', 'Sanger / Illumina 1.9'],\n# ['Total Sequences', 1571332],\n# ['Filtered Sequences', 0],\n# ['Sequence length', 29],\n# ['%GC', 53]],\n# 'fieldnames': ['Measure', 'Value'],\n# 'name': 'Basic Statistics',\n# 'status': 'pass'}\n\n# 'data' contains the tabular data from the module as a list of lists, with\n# numerical values cast to ints and floats as appropriate\n\n# 'fieldnames' contains the names of each column in 'data'\n\n# 'name' is the name of the module, same as the key\n\n# 'status' is pass/warn/fail as reported by fastqc\n\n# 'addnl' contains extra fields for some modules\n```\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://bitbucket.org/bubioinformaticshub/fastqcparser", "keywords": "bioinformatics fastqc parsing", "license": "", "maintainer": "Adam Labadorf", "maintainer_email": "labadorf@bu.edu", "name": "fastqcparser", "package_url": "https://pypi.org/project/fastqcparser/", "platform": "", "project_url": "https://pypi.org/project/fastqcparser/", "project_urls": { "Homepage": "http://bitbucket.org/bubioinformaticshub/fastqcparser" }, "release_url": "https://pypi.org/project/fastqcparser/1.1/", "requires_dist": null, "requires_python": "", "summary": "python API for parsing FastQC output", "version": "1.1" }, "last_serial": 4544798, "releases": { "1.0": [ { "comment_text": "", 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