Metadata-Version: 1.1
Name: capsid
Version: 1.4.2
Summary: CaPSID: Computational Pathogen Sequence Identification
Home-page: https://github.com/capsid/capsid
Author: Shane Wilson
Author-email: shane.wilson@oicr.on.ca
License: GNU General Public License, Version 3.0
Download-URL: https://github.com/capsid/capsid
Description: CaPSID
        ========
        **CaPSID** (Computational Pathogen Sequence IDentification) is a comprehensive
        open source platform which integrates a high-performance computational pipeline
        for pathogen sequence identification and characterization in human genomes and
        transcriptomes together with a scalable results database and a user-friendly
        web-based software application for managing, querying and visualizing results.
        
        **Project Leader** Vincent Ferretti
        
        **Development Team** Ivan Borozan, Philippe Laflamme, Shane Wilson
        
        Downloading and using **CaPSID** is free, if you use **CaPSID** or its code in your
        work please acknowledge **CaPSID** by referring to its GitHub homepage https://github.com/capsid. 
        This is important for us since obtaining grants is one significant way to fund
        planning and implementation for our project. Also if you find **CaPSID** useful
        in your research feel free to let us know.
        
        Getting Started
        ---------------
        You will need a MongoDB database, a Python 2.7 installation and a Java Web Server. For more details, read the wiki:
        
          https://github.com/capsid/capsid/wiki/
        
        License and Copyright
        ---------------------
        Licensed under the GNU General Public License, Version 3.0. See LICENSE for more details.
        
        Copyright 2011 The Ontario Institute for Cancer Research.
        
        Acknowledgement
        ---------------
        This project is supported by the Ontario Institute for Cancer Research
        (OICR) through funding provided by the government of Ontario, Canada.
        
        
        News
        ====
        
        1.4.2
        -----
        
        *Release date: 2 September 2012*
        
        * Removes MongoKit dependency
        
        1.4.1
        -----
        
        *Release date: 4 July 2012*
        
        * Fixes cursor timeout for long running statistics queries
        
        1.4.0
        -----
        
        *Release date: 1 June 2012*
        
        * Adds statistics while they are being run rather than all at the end
        * Saves unique id for genes as uid
        
        1.3.0
        -----
        
        *Release date: 28 Feb 2012*
        
        * Adds a new field in mapped for AS tag
        * Links mapped genes to NCBI page
        * Uses max sample coverage for project max coverage
        * Adds timer to wait for file collapsing to finish when intersecting
        * Using a path/to/file input no longer breaks intersecting
        
        1.2.6
        -----
        
        *Release date: 6 Feb 2012*
        
        * Subtraction filters out unmapped when building mapped reads
        
        1.2
        ---
        
        *Release date: 20 Jan 2012*
        
        * Utility to create FastQ files from unmapped reads
        * Utility to return intersection of FastQ files
        * Utility to return filter FastQ files
        * Added mapq threshold flag to subtraction
        * Gbloader can now load bacteria and fungal genomes
        * Saves genome sequences to database using GridFS
        * Reduced memory footprint when calculating statistics
        * use subprocesses instead of os.system
        * mapq scores filter needs to include 0 <= mapq <=3 due to multiple mapping reads
        
        1.1
        ---
        
        *Release date: 25 Nov 2011*
        
        * Adds support for pair-end reads
        
        1.0.1
        -----
        
        *Release date: 19 Oct 2011*
        
        * Added support for MongoDB authentication
        
        1.0
        ---
        
        *Release date: 12 Oct 2011*
        
        * Initial release
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: Unix
