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#!/usr/bin/env python
# File created on 18 Jun 2011
from __future__ import division
__author__ = "William Van Treuren"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["William Van Treuren","Greg Caporaso", "Daniel McDonald","Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "William Van Treuren"
__email__ = "vantreur@colorado.edu"
from cogent.parse.tree import DndParser
from qiime.filter import (filter_fasta, negate_tips_to_keep,
get_seqs_to_keep_lookup_from_seq_id_file,
get_seqs_to_keep_lookup_from_fasta_file,
filter_tree)
from qiime.util import parse_command_line_parameters, make_option
script_info = {}
script_info['brief_description'] = """This script prunes a tree based on a set of tip names"""
script_info['script_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)."""
script_info['script_usage'] = []
script_info['script_usage'].append(("""Prune a tree to include only the tips in tips_to_keep.txt""",\
"""""",\
"""%prog -i rep_seqs.tre -t tips_to_keep.txt -o pruned.tre"""))
script_info['script_usage'].append(("""Prune a tree to remove the tips in tips_to_remove.txt. Note that the -n/--negate option must be passed for this functionality""",\
"""""",\
"""%prog -i rep_seqs.tre -t tips_to_keep.txt -o negated.tre -n"""))
script_info['script_usage'].append(("""Prune a tree to include only the tips found in the fasta file provided""",\
"""""",\
"""%prog -i rep_seqs.tre -f fast_f.fna -o pruned_fast.tre"""))
script_info['output_description'] = \
"""Output is a pruned tree in newick format."""
script_info['required_options']=[\
make_option('-i',
'--input_tree_filepath',
action='store',
type='existing_filepath',
dest='input_tree_fp',
help='input tree filepath'),
make_option('-o',
'--output_tree_filepath',
action='store',
type='new_filepath',
dest='output_tree_fp',
help='output tree filepath'),\
]
script_info['optional_options']=[\
make_option('-n',
'--negate',
default=False,
action='store_true',
help='if negate is True will remove input tips/seqs, if \
negate is False, will retain input tips/seqs [default: %default]'),
make_option('-t',
'--tips_fp',
action='store',
type='existing_filepath',
help='A list of tips (one tip per line) or sequence identifiers \
(tab-delimited lines with a seq identifier in the first field) \
which should be retained \
[default: %default]'),
make_option('-f',
'--fasta_fp',
action='store',
type='existing_filepath',
help='A fasta file where the seq ids should be retained'
' [default: %default]'),\
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_tree_fp = opts.input_tree_fp
tips_fp = opts.tips_fp
fasta_fp = opts.fasta_fp
output_tree_fp = opts.output_tree_fp
if tips_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_seq_id_file(open(tips_fp,'U'))
elif fasta_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_fasta_file(open(fasta_fp,'U'))
else:
option_parser.error("Must provide either -t or -f.")
tree = DndParser(open(input_tree_fp,'U'))
if opts.negate:
tips_to_keep = negate_tips_to_keep(tips_to_keep, tree)
filtered_tree = filter_tree(tree,tips_to_keep)
filtered_tree.writeToFile(output_tree_fp)
if __name__ == "__main__":
# this comes in handy sometimes
# import sys
# sys.setrecursionlimit(10000)
main()
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