File: PKG-INFO

package info (click to toggle)
python-airr 1.2.1-2
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 272 kB
  • sloc: python: 1,470; sh: 19; makefile: 10
file content (67 lines) | stat: -rw-r--r-- 2,683 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
Metadata-Version: 1.1
Name: airr
Version: 1.2.1
Summary: AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data.
Home-page: http://docs.airr-community.org
Author: AIRR Community
Author-email: UNKNOWN
License: CC BY 4.0
Description: AIRR Python Reference Library
        ===============================================================================
        
        **Installation**
        
        Install in the usual manner from PyPI::
        
            > pip3 install airr --user
        
        Or from the `downloaded <https://github.com/airr-community/airr-standards>`__
        source code directory::
        
            > python3 setup.py install --user
        
        **Reading AIRR formatted files**
        
        The ``airr`` package contains functions to read and write AIRR data files
        as either iterables or pandas data frames. The usage is straightforward,
        as the file format is a typical tab delimited file, but the package
        performs some additional validation and type conversion beyond using a
        standard CSV reader.
        
        .. code-block:: python
        
            import airr
        
            # Create an iteratable that returns a dictionary for each row
            reader = airr.read_rearrangement('input.tsv')
        
            # Load the entire file into a pandas data frame
            df = airr.load_rearrangement('input.tsv')
        
        **Writing AIRR formatted files**
        
        Similar to the read operations, write functions are provided for either creating
        a writer class to perform row-wise output or writing the entire contents of
        a pandas data frame to a file. Again, usage is straightforward with the `airr`
        output functions simply performing some type conversion and field ordering
        operations.
        
        .. code-block:: python
        
            import airr
        
            # Create a writer class for iterative row output
            writer = airr.create_rearrangement('output.tsv')
            for row in reader:  writer.write(row)
        
            # Write an entire pandas data frame to a file
            airr.dump_rearrangement(df, 'file.tsv')
        
Keywords: AIRR,bioinformatics,sequencing,immunoglobulin,antibody,adaptive immunity,T cell,B cell,BCR,TCR
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics