README.md

iCUB

Information theory based codon usage bias This python script calculates iCUB of a given sequence.

Parameters to run iCUB in terminal:

    $ python nullseq.py [-h] [-s] [Sinput] [-o] [-t] [-b] [-e]

Argument	Description	Other
-s	Change to single nucleotide sequence mode	Optional
Sinput	path/to/fasta/file or nucleotide sequence if using -m flag
-o	/output/file/Path	Default: calculated_icub.csv
-t TransTable	NCBI translation table	Default: 11
-b	input sequenes do not inlcude start codons	Optional
-e	input sequenes do not inlcude stop codons	Optional

Example:

1. Calculate iCUB for a single nucleotide seqeunce:

    $ python iCUB.py -s nucloeotidesequence
   

   specifications on the sequence can be added using the -b -e and -t flags

    $ python iCUB.py -sbe nucloeotidesequence -t 10
   

   the above indicates that the sequence should be calculated using the translation table 10 and that the sequence does not have stop or start codon in it

2. Calculate iCUB for nucleotide sequences in a fasta file

    $ python iCUB.py /path/to/fasta/file
   

   specifications regarding the sequences can be added using the -b -e and -t flags

     $ python iCUB.py -be /path/to/fasta/file -t 10 -o /path/to/output/file
   

   the above indicates that all sequences should be calculated using the translation table 10 and that the sequences do not have stop or start codon in it and the file with the calcualted iCUB should be saved to /path/to/output/file

Using iCUB as a package:

    >>> import iCUB as iCUB
    >>> nucleotidesequence = "ATG...TGG"
    >>> iCUB.iCUB_Calculator(nucleotidesequence).get_iCUB()

If the sequences does not have start or stop codons or does not use translation table 11, additonal attributes will need to be specified

Using other translation tables:

    >>> tanslationtable = 5
    >>> iCUB.iCUB_Calculator(nucleotidesequence, n=translationtable).get_iCUB()

Sequences without start codons:

    >>> nucleotidesequence = "GCG...TGG"
    >>> iCUB.iCUB_Calculator(nucleotidesequence, start=False).get_iCUB()

Sequences without stop codons:

    >>> nucleotidesequence = "ATG...AAA"
    >>> iCUB.iCUB_Calculator(nucleotidesequence, stop=False).get_iCUB()