bed-reader 0.0.5a0

Bed Reader

bed-reader

A simple and efficient PLINK .bed file format reader and writer.

Also, efficiently reads slices of data and accesses individual (sample) and SNP (variant) properties.

Examples

Read everything in a .bed file.

>>> import numpy as np
>>> from bed_reader import open_bed, sample_file
>>> file_name = sample_file("small.bed")
>>> bed = open_bed(file_name)
>>> val = bed.read()
>>> print(val)
[[ 1.  0. nan  0.]
 [ 2.  0. nan  2.]
 [ 0.  1.  2.  0.]]
>>> del bed

Read a slice: every 2nd individual (sample) and SNP (variant) index position 20 (inclusive) to 30 (exclusive).

>>> file_name2 = sample_file("some_missing.bed")
>>> bed2 = open_bed(file_name2)
>>> val2 = bed2.read(index=np.s_[::2,20:30])
>>> print(val2.shape)
(50, 10)
>>> del bed2

List the first 5 individual (sample) ids, the first 5 SNP (variant) ids, and every unique chromosome. Then, read every value in chromosome 5.

>>> with open_bed(file_name2) as bed3:
...     print(bed3.iid[:5])
...     print(bed3.sid[:5])
...     print(np.unique(bed3.chromosome))
...     val3 = bed3.read(index=np.s_[:,bed3.chromosome=='5'])
...     print(val3.shape)
['iid_0' 'iid_1' 'iid_2' 'iid_3' 'iid_4']
['sid_0' 'sid_1' 'sid_2' 'sid_3' 'sid_4']
['1' '10' '11' '12' '13' '14' '15' '16' '17' '18' '19' '2' '20' '21' '22'
 '3' '4' '5' '6' '7' '8' '9']
(100, 6)

#cmk Doc test python -m doctest -v README.md

Documentation

• Documentation with examples.
• Project Home and Full Annotated Bibliography

Code

• PyPi
• GitHub

Contacts

• Email the developers at [e-mail].
• Join the user discussion and announcement list (or use web sign up).
• Open an issue on GitHub.

Quick install:

If you have pip installed, installation is as easy as:

pip install bed-reader

Detailed Package Install Instructions: #cmk need this???

pysnptools has the following dependencies:

python 3.7 or 3.8

Package(s):

• numpy

(1) Installing from source

Go to the directory where you copied the source code for bed-reader

On Linux:

At the shell, type:

sudo python setup.py install

On Windows:

At the OS command prompt, type

python setup.py install

For developers (and also to run regression tests)

pip install -r requirements-dev.txt

When working on the developer version, first add the src directory of the package to your PYTHONPATH environment variable.

To build extension (from .\src dir), type the following at the OS prompt:

python setup.py build_ext --inplace

Don't forget to set your PYTHONPATH to point to the directory above the one named bed-reader in the bed-reader source code. For e.g. if bed-reader is in the [somedir] directory, then in the Unix shell use:

export PYTHONPATH=$PYTHONPATH:[somedir]

Or in the Windows DOS terminal, one can use:

set PYTHONPATH=%PYTHONPATH%;[somedir]

Note for Windows: You must have Visual Studio installed.

Running regression tests

From the directory tests at the top level, run:

pytest

This will run a series of regression tests.

Note that you must use "python setup.py build_ext --inplace" to run the regression tests, and not "python setup.py install".