ruwaa-mohamed/x_count

x_count

A standalone Python tool that counts the number of 'X' characters per sequence in a multi-FASTA file and return the results in CSV format.

How to install

gh repo clone ruwaa-mohamed/x_count

How to use

python3 x_count/x_count.py -f <path/to/file_in.fasta> -o <path/to/file_out.csv>

Example

python3 x_count/x_count.py -f input.fasta -o output.csv

Main Arguments

• -f <fasta_file>: the path to the input FASTA file. It can handle multi-FASTA file where each record is composed of two lines (header and sequence). It doesn't work on FASTA file with sequence spanning multiple lines (fixed-width FASTA files).
• -o <output_file>: the path to the output CSV file.
• -h | --help: to print the help message of the tool (the user manual).

Date last modified

Nov. 02, 2021