nuc_codes

A simple tool to help convert those pesky gene-coordinates to genome coordinates.

Quickstart: Install globally or in an environment, I don't care what matters is that you use python >3.7

First clone the repository and cd into it, then:

pip install .

Let it install Then follow the help messages by entering nuc_codes help.

Then to initialize a project

nuc_codes init reference_fasta.fa reference_gff.gff project_name

You will then not have to specify a fasta and gff each time you run nuc_codes.

Then to list attributes you can query your sequence for, which come from the gff file enter:

nuc_codes project attributes

This will display all of the attribute keys in your gff file for you to query, it is best to already be familiar with what values those keys may hold in your gff.

Then to convert positions enter:

nuc_codes project gff_attribute gff_value position_1 etc.

You can enter multiple positions or just one, the full help message is as follows:

nuc_code help options A program to help Cody and hopefully make him help me more.

Initialize Program to save a gff and reference sequence. nuc_code init <reference_fasta> <reference_gff> <project_name>

Check possible attributes to use for gff extraction. nuc_code <project_name> attributes e.g. nuc_code <project_name> attributes

Query a gene positions, you can query one or multiple conditions nuc_code <project_name> e.g. nuc_code SARS Name orf1ab 4 5 6

Help note If no attribute is displayed check that the values you are using exist in your gff. Note of Importance: The Phase attribute of GFF file is not included in the tabulation of nucleotides. It is also assumed that the GFF being used is base 1 indexed.

Important note: Phase of the codon within the GFF file is not used in tabulation of codons

A little bit about the program: nuc_codes actually stands for Nuclear Cody, not nucleotide coordinates. Just as how in my mind gff does not stand for General Feature Format but instead Good Friends File.

Why nuclear cody you might ask: Well during this whole COVID-19 debacle we were tasked with tallying various mutations from variants of concern (This was awful). There multiple different reference sequences and gff files for the reference sequence, and most literature would only cite gene coordinates which were not always the easiest to convert.

Needless to say this made Cody go Nuclear! Everytime he saw gene coordinates, it was like watching two beryllium spheres over a plutonium-gallium core. Which was understandable, as it is an incredibly frustrating excercise and Cody is incredibly talented and would go through a rigorous process to make sure we always identified the right SNP.

Unfortunately I could not rely on Cody forever, as his attention can be fleeting and without his aid I was useless . So I did the only thing a Python developer could do.... dedicate a simple utility to them and beg them for aid.

This is the story of nuc_codes, let us hope it is enough to win his future efforts.

Note of Contribution: Dillon Barker or on github dorbarker, The setup.py would not be functioning without him