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gen_results.py
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gen_results.py
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# Copyright (C) 2012, 2013, 2016, 2019 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Generate output for PAML tests."""
from __future__ import print_function
import os.path
import sys
from Bio._py3k import range
VERSIONS = ["4_1", "4_3", "4_4", "4_4c", "4_5", "4_6", "4_7", "4_8", "4_9a",
"4_9i"]
def codeml(vers=None, verbose=False):
from Bio.Phylo.PAML import codeml
if vers is not None:
versions = [vers]
else:
versions = VERSIONS
tests = [("aa_model0", "aa_alignment.phylip", "species.tree"),
("aa_pairwise", "aa_alignment.phylip", "species.tree"),
("all_NSsites", "alignment.phylip", "species.tree"),
("branchsiteA", "alignment.phylip", "species.tree"),
("clademodelC", "alignment.phylip", "species.tree"),
("freeratio", "alignment.phylip", "species.tree"),
("ngene2_mgene02", "lysinYangSwanson2002.nuc", "lysin.trees"),
("ngene2_mgene34", "lysinYangSwanson2002.nuc", "lysin.trees"),
("pairwise", "alignment.phylip", "species.tree"),
("SE", "alignment.phylip", "species.tree"),
("m2a_rel", "alignment.phylip", "species.tree")]
for test in tests:
print(test[0])
cml = codeml.Codeml()
cml.working_dir = "temp"
ctl_file = os.path.join("Control_files",
"codeml",
'.'.join([test[0], "ctl"]))
alignment = os.path.join("Alignments", test[1])
tree = os.path.join("Trees", test[2])
cml.read_ctl_file(ctl_file)
cml.alignment = alignment
cml.tree = tree
for version in versions:
# M2a_rel (NSsites 22) was introduced in PAML 4.6
if test[0] == "m2a_rel" and int(version.split("_")[1][0]) < 6:
continue
print("\t{0}".format(version.replace('_', '.')))
if test[0] in ["ngene2_mgene02", "ngene2_mgene34"] and \
version == "4_6":
cml.tree = ".".join([cml.tree, "4.6"])
out_file = '.'.join(['-'.join([test[0], version]), "out"])
cml.out_file = os.path.join("Results", "codeml", test[0], out_file)
bin = ''.join(["codeml", version])
cml.run(command=bin, verbose=verbose, parse=False)
def baseml(vers=None, verbose=False):
from Bio.Phylo.PAML import baseml
if vers is not None:
versions = [vers]
else:
versions = VERSIONS
tests = [("model", list(range(0, 9))), ("nhomo", [1, 3, 4]),
("nparK", list(range(1, 5))), ("alpha1rho1", None), ("SE", None)]
alignment = os.path.join("Alignments", "alignment.phylip")
tree = os.path.join("Trees", "species.tree")
for test in tests:
print(test[0])
bml = baseml.Baseml()
for version in versions:
print("\t{0}".format(version.replace('_', '.')))
if test[1] is not None:
for n in test[1]:
if (version in ["4_3", "4_4", "4_4c", "4_5"] and
test[0] == "nparK" and n in [3, 4]):
continue
print("\t\tn = {0}".format(n))
ctl_file = (os.path.join("Control_files", "baseml",
"{0}{1}.ctl".format(test[0], n)))
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = "{0}{1}-{2}.out".format(test[0], n, version)
bml.out_file = (os.path.join("Results", "baseml", test[0],
out_file))
bin = "baseml{0}".format(version)
bml.run(command=bin, verbose=verbose, parse=False)
else:
if (version in ["4_3", "4_4", "4_4c", "4_5"] and
test[0] == "alpha1rho1"):
continue
ctl_file = (os.path.join("Control_files", "baseml",
"{0}.ctl".format(test[0])))
bml.read_ctl_file(ctl_file)
bml.alignment = alignment
bml.tree = tree
out_file = "{0}-{1}.out".format(test[0], version)
bml.out_file = (os.path.join("Results", "baseml", test[0],
out_file))
bin = "baseml{0}".format(version)
bml.run(command=bin, verbose=verbose, parse=False)
def yn00(vers=None, verbose=False):
from Bio.Phylo.PAML import yn00
if vers is not None:
versions = [vers]
else:
versions = VERSIONS
tests = ["yn00", "yn00_long", "yn00_dotted", "yn00_dottednum"]
for test in tests:
print(test)
yn = yn00.Yn00()
for version in versions:
print("\t{0}".format(version.replace('_', '.')))
ctl_file = (os.path.join("Control_files", "yn00",
"{0}.ctl".format(test)))
yn.read_ctl_file(ctl_file)
out_file = "{0}-{1}.out".format(test, version)
yn.out_file = os.path.join("Results", 'yn00', out_file)
bin = "yn00{0}".format(version)
yn.run(command=bin, verbose=verbose, parse=False)
def print_usage():
versions = ", ".join(vers.replace("_", ".") for vers in VERSIONS)
usage = """Usage: gen_results.py [-v] PROGRAM [VERSION]
Generate result files to be used in Bio.Phylo.PAML unit tests.
-v Use verbose output
PROGRAM codeml, baseml or yn00
VERSION %s
To use this, the PAML programs must be in your executable path and
they must be named programX_Y, where X and Y are the version numbers
(i.e. baseml4_5 or codeml4_4c). If VERSION is not specified, test
results will be generated for all versions listed above.
""" % (versions)
sys.exit(usage)
if __name__ == "__main__":
programs = ["codeml", "baseml", "yn00"]
prog = None
verbose = False
vers = None
if len(sys.argv) < 2:
print_usage()
for arg in sys.argv[1:]:
if arg == "-v":
verbose = True
elif arg in programs:
if prog is not None:
print("Only one program at a time, please.")
print_usage()
prog = arg
elif arg.replace(".", "_") in VERSIONS:
if vers is not None:
print("Only one version at a time, sorry.")
vers = arg.replace(".", "_")
else:
print("Unrecognized argument")
print_usage()
if prog is None:
print("No program specified")
print_usage()
if prog == "codeml":
codeml(vers, verbose)
elif prog == "baseml":
baseml(vers, verbose)
elif prog == "yn00":
yn00(vers, verbose)