def test_main_fastme(capsys):
"""
Test that when giving the alignment file, running with fastme, no bootstraps,
it creates expected files
"""
outdir = GENEPATH
soft = "fastme"
model = None
threads = None
boot = 100
cmd = "cmd: test_main_quicktree"
tree.main(cmd,
ALIGNMENT,
outdir,
soft,
model,
threads,
boot=boot,
verbose=16,
write_boot=True)
# Check output files
# phylip alignments
phylip = os.path.join(outdir, "exp_pers4genomes.grp.aln.phylip")
assert os.path.isfile(phylip)
# fastme logfile
log_file = phylip + ".fastme.log"
assert os.path.isfile(log_file)
with open(log_file, "r") as logf:
fastme_lines = logf.readlines()
assert "Input data type DNA" in " ".join(fastme_lines)
assert "evolutionary model TN93" in " ".join(fastme_lines)
# tree file
tree_file = phylip + ".fastme_tree.nwk"
assert os.path.isfile(tree_file)
assert not tutils.is_tree_lengths(tree_file)
assert tutils.is_tree_bootstrap(tree_file)
# bootstrap file
tree_boot_file = phylip + ".fastme_bootstraps.nwk"
assert os.path.isfile(tree_boot_file)
with open(tree_boot_file, "r") as tbf:
lines = tbf.readlines()
assert len(lines) == boot
# log files
logs_base = os.path.join(outdir, "PanACoTA-tree-fastme.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".details")
assert os.path.isfile(logs_base + ".debug")
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
assert "Converting fasta alignment to PHYLIP-relaxed format." in out
assert "Running FastME..." in out
assert (
"fastme -i test/data/tree/generated_by_func_tests/exp_pers4genomes.grp.aln.phylip "
"-dT -nB -s -b 100 -o test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.phylip.fastme_tree.nwk "
"-I test/data/tree/generated_by_func_tests/exp_pers4genomes.grp.aln.phylip.fastme.log "
"-B test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.phylip.fastme_bootstraps.nwk") in out
assert "END" in out
def test_main_quicktree_notverbose(capsys):
"""
Test that when giving the alignment file, running with quicktree, no bootstraps,
it creates expected files
"""
outdir = GENEPATH
soft = "quicktree"
model = None
threads = 1
cmd = "cmd: test_main_quicktree"
tree.main(cmd, ALIGNMENT, outdir, soft, model, threads)
# Check output files
# stockholm alignments
stockholm = os.path.join(outdir, "exp_pers4genomes.grp.aln.stockholm")
assert os.path.isfile(stockholm)
# quicktree logfile
log_file = stockholm + ".quicktree.log"
assert os.path.isfile(log_file)
with open(log_file, "r") as logf:
assert logf.readlines() == []
# tree file
tree_file = stockholm + ".quicktree_tree.nwk"
assert os.path.isfile(tree_file)
assert tutils.is_tree_lengths(tree_file)
assert not tutils.is_tree_bootstrap(tree_file)
# log files
logs_base = os.path.join(outdir, "PanACoTA-tree-quicktree.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".details")
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
assert "Converting fasta alignment to stockholm format." in out
assert "Running Quicktree..." in out
assert "END" in out
def test_main_from_parse(capsys):
"""
Test main when we give the output of the parser
run fastme with K2P model, no bootstrap
"""
import argparse
args = argparse.Namespace()
args.alignment = ALIGNMENT
args.boot = None
args.outdir = GENEPATH
args.soft = "iqtree"
args.model = "HKY"
args.write_boot = False
args.threads = 1
args.verbose = 2
args.quiet = False
args.memory = False
args.fast = False
args.argv = "PanACoTA tree test_main_from_parse"
tree.main_from_parse(args)
# Check output files
# iqtree log file
iq_log_file = os.path.join(GENEPATH,
"exp_pers4genomes.grp.aln.iqtree_tree.log")
assert os.path.isfile(iq_log_file)
with open(iq_log_file, "r") as logf:
iq_lines = logf.readlines()
assert (
"Command: iqtree -s test/data/align/exp_files/exp_pers4genomes.grp.aln -nt 1 "
"-m HKY -st DNA -pre test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.iqtree_tree -quiet") in " ".join(iq_lines)
assert ("Alignment has 4 sequences with 6438 columns, "
"81 distinct patterns") in " ".join(iq_lines)
assert "Analysis results written to:" in " ".join(iq_lines)
# Tree file
tree_file = os.path.join(GENEPATH,
"exp_pers4genomes.grp.aln.iqtree_tree.treefile")
assert os.path.isfile(tree_file)
assert tutils.is_tree_lengths(tree_file)
assert not tutils.is_tree_bootstrap(tree_file)
# Panacota log file
logs_base = os.path.join(GENEPATH, "PanACoTA-tree-iqtree.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
assert "Running IQtree..." in out
assert (
"IQtree command: iqtree -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-nt 1 -m HKY -st DNA -pre test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.iqtree_tree -quiet") in out
assert "END" in out
def test_main_fasttree(capsys):
"""
Test that when giving the alignment file, running with fasttree, no bootstraps,
it creates expected files
"""
outdir = GENEPATH
soft = "fasttree"
model = "-gtr"
threads = 1
boot = 100
cmd = "cmd: test_main_fasttree"
tree.main(cmd,
ALIGNMENT,
outdir,
soft,
model,
threads,
boot=boot,
verbose=2)
# Check output files
# fastme logfile
log_file = os.path.join(outdir, "exp_pers4genomes.grp.aln.fasttree.log")
assert os.path.isfile(log_file)
with open(log_file, "r") as logf:
fasttree_lines = logf.readlines()
assert "Read 4 sequences, 6438 positions" in " ".join(fasttree_lines)
assert "TreeCompleted" in " ".join(fasttree_lines)
assert ("Nucleotide distances: Jukes-Cantor Joins: balanced Support: "
"Local boot 100") in " ".join(fasttree_lines)
# tree file
tree_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.fasttree_tree.nwk")
assert os.path.isfile(tree_file)
assert not tutils.is_tree_lengths(tree_file)
assert tutils.is_tree_bootstrap(tree_file)
# log files
logs_base = os.path.join(outdir, "PanACoTA-tree-fasttree.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".details")
assert not os.path.isfile(logs_base + ".debug")
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
print(out)
assert "Running FasttreeMP..." in out
assert (
"Fasttree command: FastTreeMP -nt -gtr -noml -nocat -boot 100 "
"-log test/data/tree/generated_by_func_tests/exp_pers4genomes.grp.aln.fasttree.log "
"test/data/align/exp_files/exp_pers4genomes.grp.aln") in out
assert "END" in out
def test_main_default(capsys):
"""
Test that when giving the alignment file, and all default parameters, it runs iqtree,
and returns expected files
"""
outdir = GENEPATH
soft = "iqtree"
model = "GTR"
threads = 1
verbose = 3
cmd = "cmd test_main_default"
tree.main(cmd, ALIGNMENT, outdir, soft, model, threads, verbose=verbose)
# Check output files
iq_log_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.iqtree_tree.log")
assert os.path.isfile(iq_log_file)
with open(iq_log_file, "r") as logf:
iq_lines = logf.readlines()
assert (
"Command: iqtree -s test/data/align/exp_files/exp_pers4genomes.grp.aln -nt 1 "
"-m GTR -st DNA -pre test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.iqtree_tree -quiet") in " ".join(iq_lines)
assert ("Alignment has 4 sequences with 6438 columns, "
"81 distinct patterns") in " ".join(iq_lines)
assert "Analysis results written to:" in " ".join(iq_lines)
tree_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.iqtree_tree.treefile")
assert os.path.isfile(tree_file)
assert tutils.is_tree_lengths(tree_file)
assert not tutils.is_tree_bootstrap(tree_file)
logs_base = os.path.join(outdir, "PanACoTA-tree-iqtree.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".err")
# Check logs
out, err = capsys.readouterr()
print(out)
assert "Running IQtree..." in out
assert (
"IQtree command: iqtree -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-nt 1 -m GTR -st DNA -pre test/data/tree/generated_by_func_tests/"
"exp_pers4genomes.grp.aln.iqtree_tree -quiet") in out
assert "END" in out
def test_main_iqtree2_test_model(capsys):
"""
Test that when giving the alignment file, and all default parameters, it runs iqtree2,
and returns expected files
"""
outdir = os.path.join(GENEPATH, "test_iqtree2_testmodel")
soft = "iqtree2"
model = "TEST"
threads = 1
cmd = "cmd test_main_default"
tree.main(cmd,
ALIGNMENT,
outdir,
soft,
model,
threads,
boot=1000,
write_boot=True,
verbose=2)
# Check output files
# Check iqtree logfile
iq_log_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.iqtree_tree.log")
assert os.path.isfile(iq_log_file)
with open(iq_log_file, "r") as logf:
iq_lines = logf.readlines()
assert (
"Command: iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-T 1 -m TEST -B 1000 --boot-trees --seqtype DNA "
"--prefix test/data/tree/generated_by_func_tests/"
"test_iqtree2_testmodel/exp_pers4genomes.grp.aln.iqtree_tree "
"--quiet") in " ".join(iq_lines)
assert ("Alignment has 4 sequences with 6438 columns, "
"81 distinct patterns") in " ".join(iq_lines)
assert "Analysis results written to:" in " ".join(iq_lines)
assert "ModelFinder will test up to" in " ".join(iq_lines)
# Check treefile
tree_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.iqtree_tree.treefile")
assert os.path.isfile(tree_file)
assert not tutils.is_tree_lengths(tree_file)
assert tutils.is_tree_bootstrap(tree_file)
# Check bootstrap tree file
boot_file = os.path.join(outdir,
"exp_pers4genomes.grp.aln.iqtree_tree.ufboot")
assert os.path.isfile(tree_file)
with open(boot_file, "r") as tbf:
lines = tbf.readlines()
assert len(lines) == 1000
# Check panacota logfile
logs_base = os.path.join(outdir, "PanACoTA-tree-iqtree2.log")
assert os.path.isfile(logs_base)
assert os.path.isfile(logs_base + ".err")
assert os.path.isfile(logs_base + ".details")
# Check logs
out, err = capsys.readouterr()
assert "Running IQtree..." in out
assert (
"IQtree command: iqtree2 -s test/data/align/exp_files/exp_pers4genomes.grp.aln "
"-T 1 -m TEST -B 1000 --boot-trees --seqtype DNA --prefix test/data/tree/"
"generated_by_func_tests/test_iqtree2_testmodel/exp_pers4genomes.grp.aln.iqtree_tree "
"--quiet") in out
assert "END" in out