filter_fasta.py – This script can be applied to remove sequences from a fasta file based on input criteria.

Description:

Usage: filter_fasta.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --input_fasta_fp

Path to the input fasta file

-o, --output_fasta_fp

The output fasta filepath

[OPTIONAL]

-m, --otu_map

An OTU map where sequences ids are those which should be retained

-s, --seq_id_fp

A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained

-a, --subject_fasta_fp

A fasta file where the seq ids should be retained.

-p, --seq_id_prefix

Keep seqs where seq_id starts with this prefix

-n, --negate

Discard passed seq ids rather than keep passed seq ids [default: False]

--mapping_fp

Mapping file path (for use with –valid_states) [default: None]

--valid_states

Description of sample ids to retain (for use with –mapping_fp) [default: None]

Output:

Keep all sequences that show up in an OTU map:

filter_fasta.py -f inseqs.fasta -o filtered_seqs.fasta -m uclust_ref_otus.txt

Discard all sequences that show up in chimera checking output. NOTE: It is very important to pass -n here as this tells the script to negate the request, or discard all sequences that are listed via -s. This is necessary to remove the identified chimeras from inseqs.fasta:

filter_fasta.py -f inseqs.fasta -o non_chimeric_seqs.fasta -s chimeric_seqs.txt -n

Keep all sequences listed in a text file:

filter_fasta.py -f inseqs.fasta -o filtered_seqs.fasta -s seqs_to_keep.txt