{ "info": { "author": "Jiawei Wang", "author_email": "jerryeah@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Education", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: POSIX :: Linux", "Operating System :: Unix", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "MotifScan\n=========\n\n|pypi| |license|\n\n.. |pypi| image:: https://img.shields.io/pypi/v/motifscan.svg\n :target: https://pypi.python.org/pypi/motifscan\n\n.. |license| image:: https://img.shields.io/pypi/l/MAnorm.svg\n :target: https://github.com/shao-lab/MAnorm/blob/master/LICENSE\n\nIntroduction\n------------\n\nMotifScan is a precise and easy-use motif discovery tool based on given motifs. To search for candidate motif targets\nin given DNA sequences, the program scans them with a window of the same length as the motif, and defined raw motif\nscore of the sequence S in window as the ratio of the probability to observe target sequence S given the motif's\nPosition Weight Matrix (PWM) M and the probability to observe S given the genome background B. For each annotated motif,\nwe modeled the genome background distribution of motif score by randomly sampling the genome for 10^6 times, and defined\nthe targets of this motif as those candidates whose motif score was higher than the cutoff. And the enrichment of each\nmotif was represented by the ratio of motif target densities at input regions compared to random control regions,\ntogether with a p-value calculated from hypergeometric distribution. It is noticeable that MotifScan is not a\nde novo motif discovery tool.\n\nDocumentation\n-------------\n\nTo see the full documentation of MotifScan, please refer to: http://bioinfo.sibs.ac.cn/shaolab/motifscan/index.php\n\nInstallation\n------------\n\nThe latest version release of MotifScan is available at\n`PyPI `__:\n\n::\n\n $ pip install motifscan\n\nMotifScan uses `setuptools `__ for installation from source code.\nThe source code of MotifScan is hosted on GitHub: https://github.com/shao-lab/MotifScan\n\nYou can clone the repo and execute the following command under source directory:\n\n::\n\n $ python setup.py install\n\nUsage\n-----\n\nBuild genomes\n^^^^^^^^^^^^^\n\nBefore you use MotifScan, you need to build the prerequisites for corresponding genome assembly.\n\n::\n\n $ genomecompile [-h] [-v] -G sequences.fa -o output_dir\n\nA directory contaning compiled genome sequence and information would be generated by this command.\n\n**Note:** You only need run it once for each genome.\n\nBuild motif PWM (Optional)\n^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n**Note:** MotifScan provides some preprocessed motif PWM files under data/motif of the package.\n\nIF you have some motifs that have not be included in our pre-complied motif collection, you need to compile on your own by using the following command.\n\n::\n\n $ motifcompile \u2013M motif_pwm_demo.txt \u2013g hg19_for_motifscan\n\n-M motif raw matrix file\n\n-g a pre-compiled genome directory generated by genomecompile\n\nMotif raw matrix file should follow the format as below:\n\nmotif id and motif name are followed by a positive weighted matrix, and columns are seperated by tabs.\n::\n >MA0599.1 KLF5\n 1429 0 0 3477 0 5051 0 0 0 3915\n 2023 11900 12008 9569 13611 0 13611 13611 13135 5595\n 7572 0 0 0 0 5182 0 0 0 0\n 2587 1711 1603 565 0 3378 0 0 476 4101\n\nScan Motifs\n^^^^^^^^^^^\n\nSearch regions (-p), compiled motif PWM (-m) and genome (-g) are required for a common MotifScan task.\nAnd we recommend you to specify the gene annotation file (RefSeq) via option -t. With all these files prepared, use the following command to perform the program.\n\n::\n\n $ motifscan -p peaks.bed \u2013m motif_pwm_demo.txt \u2013g hg19_for_motifscan\n\n**Note:** Using -h/--help for the details of all arguments.\n\n\nLicense\n-------\n\n`BSD 3-Clause\nLicense `__", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://bioinfo.sibs.ac.cn/shaolab/motifscan", "keywords": "", "license": "GPLv3", "maintainer": "Hayden Sun", "maintainer_email": "sunhongduo@picb.ac.cn", "name": "motifscan", "package_url": "https://pypi.org/project/motifscan/", "platform": "", "project_url": "https://pypi.org/project/motifscan/", "project_urls": { "Homepage": "http://bioinfo.sibs.ac.cn/shaolab/motifscan" }, "release_url": "https://pypi.org/project/motifscan/1.1.2/", "requires_dist": null, "requires_python": "", "summary": "A motif discovery package developed by Shao lab in SIBS, CAS", "version": "1.1.2" }, "last_serial": 4187880, "releases": { "1.1": [ { "comment_text": "", "digests": { "md5": "38f1e481da062719fd7ae6002b3b4634", "sha256": "e325d50e3a4aecbb772ff7a885190cd93305bb33fef18baa538fa2b038642284" }, "downloads": -1, "filename": "motifscan-1.1.tar.gz", "has_sig": false, "md5_digest": "38f1e481da062719fd7ae6002b3b4634", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 11461120, "upload_time": "2017-10-22T14:04:21", "url": "https://files.pythonhosted.org/packages/e4/ad/c99471abe222aa7fc17ca8f6cf272f96e137a877dab8a8b146049b0d8bb5/motifscan-1.1.tar.gz" } ], "1.1.2": [ { "comment_text": "", "digests": { "md5": "8f104fe176005ca482c9d32ac5393877", "sha256": "7ba31fed062fc1d228ac9178383dc12711bf4f65d98ade383eccf23a4abe0099" }, "downloads": -1, "filename": "motifscan-1.1.2.tar.gz", "has_sig": false, "md5_digest": "8f104fe176005ca482c9d32ac5393877", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 11448438, "upload_time": "2018-08-20T10:19:52", "url": "https://files.pythonhosted.org/packages/12/fc/0974ba6cbffbbd9d6d4fd6e69f433d3a22c9936d2f85ff01f8d7e573bed9/motifscan-1.1.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "8f104fe176005ca482c9d32ac5393877", "sha256": "7ba31fed062fc1d228ac9178383dc12711bf4f65d98ade383eccf23a4abe0099" }, "downloads": -1, "filename": "motifscan-1.1.2.tar.gz", "has_sig": false, "md5_digest": "8f104fe176005ca482c9d32ac5393877", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 11448438, "upload_time": "2018-08-20T10:19:52", "url": "https://files.pythonhosted.org/packages/12/fc/0974ba6cbffbbd9d6d4fd6e69f433d3a22c9936d2f85ff01f8d7e573bed9/motifscan-1.1.2.tar.gz" } ] }