Skip to main content

AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data.

Project description

Installation

Install in the usual manner from PyPI:

> pip3 install airr --user

Or from the downloaded 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.

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.

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')

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

airr-1.2.1.tar.gz (35.3 kB view details)

Uploaded Source

File details

Details for the file airr-1.2.1.tar.gz.

File metadata

  • Download URL: airr-1.2.1.tar.gz
  • Upload date:
  • Size: 35.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.9.1 pkginfo/1.3.2 requests/2.18.4 setuptools/39.2.0 requests-toolbelt/0.8.0 tqdm/4.19.6 CPython/3.6.6

File hashes

Hashes for airr-1.2.1.tar.gz
Algorithm Hash digest
SHA256 b6c523cee7822b327bfcc637e6261bda27a0d4148bc46a73fef745199ee5fcb9
MD5 66f13422ea75f9b40b86acf6fd521fdd
BLAKE2b-256 7cf8af74bb65a915a717387a7f0c3311dd10cdaa00f9b8e6c13fb4cdb480d7eb

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page