filter_tree.py – This script prunes a tree based on a set of tip names

Description:

This script takes a tree and a list of OTU IDs (in one of several supported formats) and outputs a subtree retaining only the tips on the tree which are found in the inputted list of OTUs (or not found, if the –negate option is provided).

Usage: filter_tree.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_tree_fp

Input tree filepath

-o, --output_tree_fp

Output tree filepath

[OPTIONAL]

-n, --negate

If negate is not false will prune tips fed in and save all others [default: False]

-t, --tips_fp

A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained [default: None]

-f, --fasta_fp

A fasta file where the seq ids should be retained [default: None]

Output:

Output is a pruned tree in newick format.

Prune a tree to include only the tips in tips_to_keep.txt:

filter_tree.py -i rep_seqs.tre -t tips_to_keep.txt -o rep_seqs_subtree.tre

Prune a tree to remove the tips in tips_to_remove.txt. Note that the -n/–negate option must be passed for this functionality.:

filter_tree.py -i rep_seqs.tre -t tips_to_remove.txt -o rep_seqs_subtree.tre -n