Get the human genome (hg38) coordinates of a gene
pip install hgfind
Requirements:
- Python >=3.6
hgfind can be used either on the command line or as a function within
Python
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 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'}
Any suggestions / PR requests are welcome!
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