Bekir Faydaci Ensembl Assignment

Introduction:

This tool allows you to:
1) Query the amino acid count at a specific protein sequence position, across transcripts in a given gene.
2) Query the mean count for each amino acid averaged across a protein sequence range, in a given gene.

How to use this tool:

To run the tool from the command line, enter:
$ python bekir_faydaci_ensembl_assignment.py -s <gene_symbol> -p <start_position> [-e <end_position>]

Options:

Flags	Description
-s	Gene symbol
-p	(Start) position of the protein sequence
-e	End position of the protein sequence (this position included)
-h/--help	Prints help message

Example runs:

$ python bekir_faydaci_ensembl_assignment.py -s BRCA2 -p 1

Fetching data for: BRCA2
At position: 1
AA 	Count
-- 	-----
M	5.0
X	2.0
S	1.0
V	1.0

The amino acid with the highest count is M, with a count of 5.

$ python bekir_faydaci_ensembl_assignment.py -s BRCA2 -p 1 -e 100

Fetching data for: BRCA2
At range: 1 - 100
AA 	Mean count
-- 	----------
S	0.52
L	0.46
P	0.43
K	0.41
E	0.39
T	0.27
Q	0.27
I	0.26
F	0.26
N	0.24
V	0.24
A	0.23
D	0.2
G	0.18
R	0.16
Y	0.16
C	0.1
H	0.1
M	0.05
W	0.05
X	0.02

The amino acid with highest mean count is S, with a mean count of 0.52.
Some of the transcripts are out of range at the specified position,
only the data for 5/9 transcripts are shown.

Dependencies:

The tool depends on the python module requests, to install this module enter the following line into the terminal:
$ python pip install requests

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Bekir Faydaci 20/02/2020