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# Copyright 2009 by Peter Cock. All rights reserved.
# 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.
#
# This unit test attempts to locate the blastall executable and the nr
# database, and if it finds them then do some standalone blast searches
# using Bio.Blast.NCBIStandalone to call the command line tool.
import os, sys
import subprocess
import unittest
from Bio import MissingExternalDependencyError
from Bio.Blast import Applications
# TODO - On windows, can we use the ncbi.ini file?
wanted = ["blastx", "blastp", "blastn", "tblastn", "tblastx",
"rpsblast", "rpstblastn", "psiblast"]
exe_names = {}
if sys.platform=="win32":
#The Windows 32 bit BLAST 2.2.22+ installer does add itself to the path,
#and by default installs to C:\Program Files\NCBI\BLAST-2.2.22+\bin
#To keep things simple, assume BLAST+ is on the path on Windows.
#
#On Windows the environment variable name isn't case senstive,
#but must split on ";" not ":"
likely_dirs = os.environ.get("PATH", "").split(";")
else :
likely_dirs = os.environ.get("PATH", "").split(":")
for folder in likely_dirs:
if not os.path.isdir(folder): continue
for name in wanted :
if sys.platform=="win32":
exe_name = os.path.join(folder, name+".exe")
else:
exe_name = os.path.join(folder, name)
if not os.path.isfile(exe_name):
continue
#To tell the old and new rpsblast apart (since I have both on
#my path and the old blast has priority), try -h as a parameter.
#This should also reject WU-BLAST (since it doesn't like -h).
child = subprocess.Popen(exe_name + " -h",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
output, error = child.communicate()
if child.returncode==0 and "ERROR: Invalid argument: -h" not in output:
exe_names[name] = exe_name
#else :
# print "Rejecting", exe_name
del exe_name, name
if len(exe_names) < len(wanted) :
raise MissingExternalDependencyError("Install the NCBI BLAST+ command line "
"tools if you want to use the "
"Bio.Blast.Applications wrapper.")
class Pairwise(unittest.TestCase):
def test_blasp(self):
"""Pairwise BLASTP search"""
global exe_names
cline = Applications.NcbiblastpCommandline(exe_names["blastp"],
query="Fasta/rose.pro",
subject="GenBank/NC_005816.faa",
evalue=1)
self.assertEqual(str(cline), exe_names["blastp"] \
+ " -query Fasta/rose.pro -evalue 1" \
+ " -subject GenBank/NC_005816.faa")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
% (return_code, cline))
self.assertEqual(10, stdoutdata.count("Query= "))
self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
#TODO - Parse it? I think we'd need to update this obsole code :(
#records = list(NCBIStandalone.Iterator(StringIO(stdoutdata),
# NCBIStandalone.BlastParser()))
def test_blastn(self):
"""Pairwise BLASTN search"""
global exe_names
cline = Applications.NcbiblastpCommandline(exe_names["blastn"],
query="GenBank/NC_005816.ffn",
subject="GenBank/NC_005816.fna",
evalue="0.000001")
self.assertEqual(str(cline), exe_names["blastn"] \
+ " -query GenBank/NC_005816.ffn -evalue 0.000001" \
+ " -subject GenBank/NC_005816.fna")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
% (return_code, cline))
self.assertEqual(10, stdoutdata.count("Query= "))
self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
#TODO - Parse it?
def test_tblastn(self):
"""Pairwise TBLASTN search"""
global exe_names
cline = Applications.NcbiblastpCommandline(exe_names["tblastn"],
query="GenBank/NC_005816.faa",
subject="GenBank/NC_005816.fna",
evalue="1e-6")
self.assertEqual(str(cline), exe_names["tblastn"] \
+ " -query GenBank/NC_005816.faa -evalue 1e-6" \
+ " -subject GenBank/NC_005816.fna")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
% (return_code, cline))
self.assertEqual(10, stdoutdata.count("Query= "))
self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
#TODO - Parse it?
class CheckCompleteArgList(unittest.TestCase):
def check(self, exe_name, wrapper) :
global exe_names
exe = exe_names[exe_name]
cline = wrapper(exe, h=True)
names = set(parameter.names[0] \
for parameter in cline.parameters)
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
stdoutdata, stderrdata = child.communicate()
self.assertEqual(stderrdata, "",
"%s\n%s" % (str(cline), stderrdata))
names_in_tool = set()
while stdoutdata :
index = stdoutdata.find("[")
if index == -1 : break
stdoutdata = stdoutdata[index+1:]
index = stdoutdata.find("]")
assert index != -1
name = stdoutdata[:index]
if " " in name : name = name.split(None,1)[0]
names_in_tool.add(name)
stdoutdata = stdoutdata[index+1:]
extra = names.difference(names_in_tool)
missing = names_in_tool.difference(names)
if "-soft_masking" in missing :
#Known issue, need to establish how this option works
missing.remove("-soft_masking")
if "-use_index" in missing :
#Known issue, need to establish how this option works
missing.remove("-use_index")
if "-verbose" in missing :
#Known issue, seems to be present in some builds (Bug 3043)
missing.remove("-verbose")
if "-remote_verbose" in missing :
#Known issue, seems to be present in some builds (Bug 3043)
missing.remove("-remote_verbose")
if "-use_test_remote_service" in missing :
#Known issue, seems to be present in some builds (Bug 3043)
missing.remove("-use_test_remote_service")
if extra or missing :
raise MissingExternalDependencyError("BLAST+ and Biopython out of sync. "
"Your version of the NCBI BLAST+ tool %s does not match what we "
"are expecting. Please update your copy of Biopython, or report "
"this issue if you are already using the latest version. "
"(Exta args: %s; Missing: %s)" \
% (exe_name, ",".join(sorted(extra)), ",".join(sorted(missing))))
#An almost trivial example to test any validation
cline = wrapper(exe, query="dummy")
str(cline)
def test_blastx(self):
"""Check all blastx arguments are supported"""
self.check("blastx", Applications.NcbiblastxCommandline)
def test_blastp(self):
"""Check all blastp arguments are supported"""
self.check("blastp", Applications.NcbiblastpCommandline)
def test_blastn(self):
"""Check all blastn arguments are supported"""
self.check("blastn", Applications.NcbiblastnCommandline)
def test_tblastx(self):
"""Check all tblastx arguments are supported"""
self.check("tblastx", Applications.NcbitblastxCommandline)
def test_tblastn(self):
"""Check all tblastn arguments are supported"""
self.check("tblastn", Applications.NcbitblastnCommandline)
def test_psiblast(self):
"""Check all psiblast arguments are supported"""
self.check("psiblast", Applications.NcbipsiblastCommandline)
def test_rpsblast(self):
"""Check all rpsblast arguments are supported"""
self.check("rpsblast", Applications.NcbirpsblastCommandline)
def test_rpstblastn(self):
"""Check all rpstblastn arguments are supported"""
self.check("rpstblastn", Applications.NcbirpstblastnCommandline)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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