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#!/usr/bin/env python
"""Tests for ParsInsert v1.03 application controller."""
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Production"
from shutil import rmtree
from cogent.util.unit_test import TestCase, main
from cogent.app.parsinsert import ParsInsert, insert_sequences_into_tree
from cogent.core.alignment import Alignment
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.tree import DndParser
from cogent.core.moltype import DNA
from cogent.app.util import get_tmp_filename
from os.path import splitext
from os import getcwd, remove, rmdir, mkdir
class ParsInsertTests(TestCase):
def setUp(self):
# create a list of files to cleanup
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
# load query seqs
self.seqs = Alignment(MinimalFastaParser(QUERY_SEQS.split()))
# generate temp filename
tmp_dir='/tmp'
self.outfile = get_tmp_filename(tmp_dir)
# create and write out reference sequence file
self.outfasta=splitext(self.outfile)[0]+'.fasta'
fastaout=open(self.outfasta,'w')
fastaout.write(REF_SEQS)
fastaout.close()
self._paths_to_clean_up.append(self.outfasta)
# create and write out starting tree file
self.outtree=splitext(self.outfile)[0]+'.tree'
treeout=open(self.outtree,'w')
treeout.write(REF_TREE)
treeout.close()
self._paths_to_clean_up.append(self.outtree)
def tearDown(self):
"""cleans up all files initially created"""
# remove the tempdir and contents
map(remove,self._paths_to_clean_up)
map(rmdir,self._dirs_to_clean_up)
def test_base_command(self):
"""Base command-calls"""
app = ParsInsert()
self.assertEqual(app.BaseCommand, \
''.join(['cd "',getcwd(),'/"; ','parsinsert']))
def test_change_working_dir(self):
"""Change working dir"""
app = ParsInsert(WorkingDir='/tmp/ParsInsertTest')
self.assertEqual(app.BaseCommand, \
''.join(['cd "','/tmp/ParsInsertTest',\
'/"; ','parsinsert']))
rmtree('/tmp/ParsInsertTest')
def test_insert_sequences_into_tree(self):
"""Inserts sequences into Tree"""
# define log fp
log_fp='/tmp/parsinsert.log'
self._paths_to_clean_up.append(log_fp)
# define tax assignment values fp
tax_assign_fp='/tmp/tax_assignments.log'
self._paths_to_clean_up.append(tax_assign_fp)
# set the reference alignment and starting tree
param={
'-t':self.outtree,
'-s':self.outfasta,
'-l':log_fp,
'-o':tax_assign_fp
}
seqs, align_map = self.seqs.toPhylip()
# insert sequences into tree
tree = insert_sequences_into_tree(seqs, DNA, params=param)
# rename tips back to query names
for node in tree.tips():
if node.Name in align_map:
node.Name = align_map[node.Name]
self.assertEqual(tree.getNewick(with_distances=True),exp_tree)
QUERY_SEQS= """\
>6
TGCATGTCAGTATAGCTTTGGTGAAACTGCGAATGGCTCATTAAATCAGT
>7
TGCATGTCAGTATAACTTTGGTGAAACTGCGAATGGCTCATTAAATCAGT
"""
REF_SEQS= """\
>seq0000011
TGCATGTCAGTATAGCTTTAGTGAAACTGCGAATGGCTCATTAAATCAGT
>seq0000012
TGCATGTCAGTATAGCTTTAGTGAAACTGCGAATGGCTNNTTAAATCAGT
>seq0000013
TGCATGTCAGTATAGCATTAGTGAAACTGCGAATGGCTCATTAAATCAGT
>seq0000014
TCCATGTCAGTATAACTTTGGTGAAACTGCGAATGGCTCATTAAATCAGG
>seq0000015
NNNNNNNNNNTATATCTTATGTGAAACTTCGAATGCCTCATTAAATCAGT
"""
REF_TREE="""((seq0000014:0.08408,seq0000015:0.13713)0.609:0.00215,seq0000013:0.02032,(seq0000011:0.00014,seq0000012:0.00014)0.766:0.00015);
"""
exp_tree = """((seq0000014:0.08408,seq0000015:0.13713,7:0.02027):0.00215,seq0000013:0.02032,(seq0000011:0.00014,seq0000012:0.00014,6:0.02027):0.00015):0.0;"""
if __name__ == '__main__':
main()
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