fix_arb_fasta.py – Reformat ARB FASTA files

Description:

This script fixes ARB FASTA formatting by repairing incorrect line break chararcters, stripping spaces and replacing ”.” with “-” characters.

Usage: fix_arb_fasta.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --input_fasta_fp

Path to the input fasta file

[OPTIONAL]

-o, --output_fp

Path where output will be written [default: print to screen]

Output:

The reformatted sequences are written to stdout or to the file path provided with -o.

Example:

Fix the input ARB FASTA format file arb.fasta and print the result to stdout:

fix_arb_fasta.py -f arb.fasta

Example saving to an output file:

Fix the input ARB FASTA format file arb.fasta and print the result to fixed.fasta:

fix_arb_fasta.py -f arb.fasta -o fixed.fasta