filter_fasta.py -f extract_no_N_200.fasta -o remain.fasta -s out.list

[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.

-b, --biom_fp

A biom file where otu identifiers 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.

--sample_id_fp

Keep seqs where seq_id starts with a sample id listed in this file. Must be newline delimited and may not contain a header.

-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]