clean_fasta.py – Filters input fasta file to remove gaps and ‘U’ characters.

Description:

This module will filter out gap characters (‘.’ and ‘-‘), spaces, and/or uracil characters (‘U’) from an input fasta file(s). The module can also capitalize the characters in the filtered file(s). This should be done for fasta files to be utilized with analyze_primers.py or any downstream module requring input fasta files.

Usage: clean_fasta.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --fasta_seqs

Target fasta file(s) to filter. Separate multiple files with a colon.

[OPTIONAL]

-o, --output_dir

Output directory for filtered fasta file(s). [default: .]

-g, --gap_chars

Filter gap characters ”.” and “-” [default: True]

-s, --space_chars

Filter space characters. [default: True]

-u, --convert_uracil

Convert Uracil “U” characters to “T”. [default: True]

-c, --cap_seqs

Capitalize filtered sequences [default: True]

Output:

Output fasta file(s) generated by this module will have a ‘_filtered.fasta’ appended to the original fasta file name.

Standard Example usage:

clean_fasta.py [options] {-f input_fasta_filepath [required] }

Keep gap characters in two aligned fasta files, but allow all other filtering:

clean_fasta.py -f input_aligned_seqs1.fasta:input_aligned_seqs2.fasta -g