Motif-search

Script to search location of motifs in fasta files.

Usage

python motif-search-v2.py [OPTIONS]

Options:

Short	Option	Type	Default	Description
-h	--help			show this help message and exit
-i	--inp	path	Required	Input fasta file
-m	--motif	string	Required	Motif to be searched
-p	--relax_perc	float	100	Relaxed percentage similarity
-o	--out	path	motif_result.txt	Output file

motif-search v2

Refactoring code for better readability, adding fixes and features.

Fixes:

1. Changing genome variable to list instead of string.
2. Option to define output file.
3. Changing code structure for better readability.

Features:

1. Added argparse instead of input.
2. Motif search on complementary strand.
3. Search motif on multiple chromosomes.

Future:

1. Option to include gaps.
2. Option to include bedfile with selected regions for motif search.
3. Multiple motif searches.
4. Levenshtein distance scoring.

motif-search v1

A simple motif search code that I wrote during my introduction to computational biology during my master's