Metadata-Version: 1.1
Name: cual-id
Version: 0.9.0
Summary: A package for creating and managing sample identifiers in comparative -omics datasets.
Home-page: https://github.com/johnchase/cual-id
Author: John Chase
Author-email: chasejohnh@gmail.com
License: UNKNOWN
Description: =======
        cual-id
        =======
        |Build Status| |Coverage Status|
        
        cual-id paper
        =============
        Preprint outlining implications and uses of cual-id.
        `cual-id globally unique, correctable, and human-friendly sample identifiers for comparative
        -omics studies <https://peerj.com/preprints/1431/>`__.
        
        Peer review is currently in progress
        
        
        Install
        =======
        
        .. code:: bash
        
            pip install cual-id
        
        
        Usage
        =====
        
        Getting help
        ------------
        
        .. code:: bash
        
           cual-id --help
        
        
        Creating a list of IDs
        ----------------------
        
        .. code:: bash
        
           cual-id create ids 42 # writes 42 ids to stdout
           cual-id create ids 42 > my-ids.txt # writes 42 ids to my-ids.txt
        
        
        
        Creating a PDF of ID labels
        ---------------------------
        
        If you need to label sample containers with stickers, you can create a
        printable PDF for those stickers. Currently the only sticker sheet format
        supported is a 4 by 9 sheet. We designed this printout for
        `Electronic Imaging Materials #80402 label sheets
        <http://barcode-labels.com/?s=80402&submit=Search>`_. When printing PDFs make
        sure to check `Actual Size` in the print dialog box.
        
        .. code:: bash
        
           cual-id create labels my-ids.txt --output-pdf my-labels.pdf
           cual-id create labels my-ids.txt --output-pdf my-labels.pdf --suppress-ids # don't print the ids, only the barcodes
           cual-id create labels my-ids.txt --output-pdf my-labels.pdf --barcode none # don't print barcodes, just the ids
        
        
        Correcting a list of ids
        ------------------------
        
        .. code:: bash
        
           cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt # report fixed, unfixable and duplicates, the default
           cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt --show FN # report only fixed and unfixable IDs
        
        Result code definitions
        ~~~~~~~~~~~~~~~~~~~~~~~
        * D: duplicate
        * F: fixed
        * N: not fixable
        * V: valid (didn't need correction)
        
        Output Format
        ~~~~~~~~~~~~~
        
        ::
        
           input-id <tab> output-id <tab> result-codes
        
        
        For example:
        
        ::
        
           1a529f8b	1a529f88	F
           d60d0e2b	d60d0c2b	F
           439628o9	43962809	F
           439628o9	43962809	DF
           df47deb4	df47deba	F
        
        
        Python API
        ----------
        
        .. code:: python
        
           from cualid import create_ids
           create_ids(10) # Creates a list of tuples containing a UUID and a cualid
        
        
        .. |Build Status| image:: https://travis-ci.org/johnchase/cual-id.svg?branch=master
           :target:  https://travis-ci.org/johnchase/cual-id
        .. |Coverage Status| image:: https://coveralls.io/repos/johnchase/cual-id/badge.svg?branch=master&service=github
           :target:  https://coveralls.io/github/johnchase/cual-id?branch=master
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Utilities
Classifier: Topic :: Scientific/Engineering
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
