hgfind 1.0.0

Convert a gene name to human genome coordinates

hgfind

Get the human genome (hg38) coordinates of a gene

Installation

pip install hgfind

Requirements:

• Python >=3.6

Usage

hgfind can be used either on the command line or as a function within Python

As a commandline tool

hgfind <gene>

where gene is a gene name such as "PTEN". The name can be a synonym as well.

A successful example:

$ hgfind auf1
HNRNPD => 4:82352498-82374503 (-)

$ echo $?
0

The result shows that HNRNPD (a synonym for AUF1) lies on chromosome 4, in the specified base interval. The (-) indicates that its transcripts all lie on the reverse strand.

Using an unrecognized name results in an error:

$ hgfind fjlsfl
fjlsfl not recognized as a gene

$ echo $?
1

As a function in Python

As an example on the Python REPL:

>>> from hgfind import hgfind
>>> hgfind("Neat2")
{'chr_n': 11, 'start_coord': 65497688, 'end_coord': 65506516, 'strand': '+', 'official_name': 'MALAT1'}

Using an unrecognized name results in an error:

>>> hgfind("gewgwre")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "hgfind.py", line 140, in hgfind
    raise WrongGeneName(
hgfind.WrongGeneName: {'message': 'The input gene could not be recognized', 'gene': 'GEWGWRE'}

Contributing

Any suggestions / PR requests are welcome!

Development

Enable recommended Git Hooks as follows:

git config --local core.hooksPath .githooks/

The above will run the following to ensure code consistency every time you commit:

• black
• isort

Also use fit-commit to ensure consistent commit message style.