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.. _filter_fasta:
.. index:: filter_fasta.py
*filter_fasta.py* -- This script can be applied to remove sequences from a fasta file based on input criteria.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
**Usage:** :file:`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
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