1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267
|
# Copyright 2008-2009 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.
#TODO - Clean up the extra files created by clustalw? e.g. *.dnd
#and *.aln where we have not requested an explicit name?
from Bio import MissingExternalDependencyError
import sys
import os
import subprocess
from Bio import Clustalw #old and obsolete
from Bio.Clustalw import MultipleAlignCL #old and obsolete
from Bio import SeqIO
from Bio import AlignIO
from Bio.Align.Applications import ClustalwCommandline #new!
#################################################################
clustalw_exe = None
if sys.platform=="win32":
#TODO - Check the path?
try:
#This can vary depending on the Windows language.
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
#Note that EBI's clustalw2 installer, e.g. clustalw-2.0.10-win.msi
#uses C:\Program Files\ClustalW2\clustalw2.exe so we should check
#for that.
#
#Some users doing a manual install have reported using
#C:\Program Files\clustalw.exe
#
#Older installers might use something like this,
#C:\Program Files\Clustalw\clustalw.exe
#
#One particular case is www.tc.cornell.edu currently provide a
#clustalw1.83 installer which uses the following long location:
#C:\Program Files\CTCBioApps\clustalw\v1.83\clustalw1.83.exe
likely_dirs = ["ClustalW2", "",
"Clustal","Clustalw","Clustalw183","Clustalw1.83",
r"CTCBioApps\clustalw\v1.83"]
likely_exes = ["clustalw2.exe",
"clustalw.exe", "clustalw1.83.exe"]
for folder in likely_dirs:
if os.path.isdir(os.path.join(prog_files, folder)):
for filename in likely_exes:
if os.path.isfile(os.path.join(prog_files, folder, filename)):
clustalw_exe = os.path.join(prog_files, folder, filename)
break
if clustalw_exe : break
else:
import commands
#Note that clustalw 1.83 and clustalw 2.0.10 don't obey the --version
#command, but this does cause them to quit cleanly. Otherwise they prompt
#the user for input (causing a lock up).
output = commands.getoutput("clustalw2 --version")
if "not found" not in output and "CLUSTAL" in output.upper():
clustalw_exe = "clustalw2"
if not clustalw_exe:
output = commands.getoutput("clustalw --version")
if "not found" not in output and "CLUSTAL" in output.upper():
clustalw_exe = "clustalw"
if not clustalw_exe:
raise MissingExternalDependencyError(\
"Install clustalw or clustalw2 if you want to use Bio.Clustalw.")
#################################################################
print "Checking error conditions"
print "========================="
print "Empty file"
input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = MultipleAlignCL(input_file, command=clustalw_exe)
try:
align = Clustalw.do_alignment(cline)
assert False, "Should have failed, returned %s" % repr(align)
except IOError, err:
print "Failed (good)"
#Python 2.3 on Windows gave (0, 'Error')
#Python 2.5 on Windows gives [Errno 0] Error
assert "Cannot open sequence file" in str(err) \
or "not produced" in str(err) \
or str(err) == "[Errno 0] Error" \
or str(err) == "(0, 'Error')", str(err)
print
print "Single sequence"
input_file = "Fasta/f001"
assert os.path.isfile(input_file)
assert len(list(SeqIO.parse(open(input_file),"fasta")))==1
cline = MultipleAlignCL(input_file, command=clustalw_exe)
try:
align = Clustalw.do_alignment(cline)
assert False, "Should have failed, returned %s" % repr(align)
except IOError, err:
print "Failed (good)"
assert "has only one sequence present" in str(err)
except ValueError, err:
print "Failed (good)"
assert str(err) == "No records found in handle"
#Ideally we'd get an IOError but sometimes we don't seem to
#get a return value from clustalw. If so, then there is a
#ValueError when the parsing fails.
print
print "Invalid sequence"
input_file = "Medline/pubmed_result1.txt"
assert os.path.isfile(input_file)
cline = MultipleAlignCL(input_file, command=clustalw_exe)
try:
align = Clustalw.do_alignment(cline)
assert False, "Should have failed, returned %s" % repr(align)
except IOError, err:
print "Failed (good)"
#Ideally we'd catch the return code and raise the specific
#error for "invalid format", rather than just notice there
#is not output file.
#Note:
#Python 2.3 on Windows gave (0, 'Error')
#Python 2.5 on Windows gives [Errno 0] Error
assert "invalid format" in str(err) \
or "not produced" in str(err) \
or str(err) == "[Errno 0] Error" \
or str(err) == "(0, 'Error')", str(err)
#################################################################
print
print "Checking normal situations"
print "=========================="
#Create a temp fasta file with a space in the name
temp_filename_with_spaces = "Clustalw/temp horses.fasta"
handle = open(temp_filename_with_spaces, "w")
SeqIO.write(SeqIO.parse(open("Phylip/hennigian.phy"),"phylip"),handle, "fasta")
handle.close()
#Create a large input file by converting another example file
#(See Bug 2804, this will produce so much output on stdout that
#subprocess could suffer a deadlock and hang). Using all the
#records should show the deadlock but is very slow - just thirty
#seems to lockup on Mac OS X, even 20 on Linux (without the fix).
temp_large_fasta_file = "temp_cw_prot.fasta"
handle = open(temp_large_fasta_file, "w")
records = list(SeqIO.parse(open("NBRF/Cw_prot.pir", "rU"), "pir"))[:40]
SeqIO.write(records, handle, "fasta")
handle.close()
del handle, records
for input_file, output_file, newtree_file in [
("Fasta/f002", "temp_test.aln", None),
("GFF/multi.fna", "temp with space.aln", None),
("Registry/seqs.fasta", "temp_test.aln", None),
("Registry/seqs.fasta", "temp_test.aln", "temp_test.dnd"),
("Registry/seqs.fasta", "temp_test.aln", "temp with space.dnd"),
(temp_filename_with_spaces, "temp_test.aln", None),
(temp_filename_with_spaces, "temp with space.aln", None),
(temp_large_fasta_file, "temp_cw_prot.aln", None),
]:
#Note that ClustalW will map ":" to "_" in it's output file
input_records = SeqIO.to_dict(SeqIO.parse(open(input_file),"fasta"),
lambda rec : rec.id.replace(":","_"))
if os.path.isfile(output_file):
os.remove(output_file)
print "Calling clustalw on %s (with %i records)" \
% (repr(input_file), len(input_records))
print "using output file %s" % repr(output_file)
if newtree_file is not None:
print "requesting output guide tree file %s" % repr(newtree_file)
#Prepare the command...
cline = MultipleAlignCL(input_file, command=clustalw_exe)
cline.set_output(output_file)
if newtree_file is not None:
cline.set_new_guide_tree(newtree_file)
#Run the command...
align = Clustalw.do_alignment(cline)
#Check the output...
print "Got an alignment, %i sequences" % (len(align))
#The length of the alignment will depend on the version of clustalw
#(clustalw 2.0.10 and clustalw 1.83 are certainly different).
output_records = SeqIO.to_dict(SeqIO.parse(open(output_file),"clustal"))
assert set(input_records.keys()) == set(output_records.keys())
for record in align:
assert str(record.seq) == str(output_records[record.id].seq)
assert str(record.seq).replace("-","") == \
str(input_records[record.id].seq)
#Clean up...
os.remove(output_file)
#Check the DND file was created.
#TODO - Try and parse this with Bio.Nexus?
if newtree_file is not None:
tree_file = newtree_file
else:
#Clustalw will name it based on the input file
tree_file = os.path.splitext(input_file)[0] + ".dnd"
assert os.path.isfile(tree_file), \
"Did not find tree file %s" % tree_file
os.remove(tree_file)
#And again, but this time using Bio.Align.Applications wrapper
#Any filesnames with spaces should get escaped with quotes automatically.
#Using keyword arguments here.
cline = ClustalwCommandline(clustalw_exe,
infile=input_file,
outfile=output_file)
assert str(eval(repr(cline)))==str(cline)
if newtree_file is not None:
#Test using a property:
cline.newtree = newtree_file
#I don't just want the tree, also want the alignment:
cline.align = True
assert str(eval(repr(cline)))==str(cline)
#print cline
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=(sys.platform!="win32"))
output, error = child.communicate()
return_code = child.returncode
assert return_code == 0
assert output.strip().startswith("CLUSTAL")
assert error.strip() == ""
align = AlignIO.read(open(output_file), "clustal")
assert set(input_records.keys()) == set(output_records.keys())
for record in align:
assert str(record.seq) == str(output_records[record.id].seq)
assert str(record.seq).replace("-","") == \
str(input_records[record.id].seq)
#Clean up...
del child
os.remove(output_file)
#Check the DND file was created.
#TODO - Try and parse this with Bio.Nexus?
if newtree_file is not None:
tree_file = newtree_file
else:
#Clustalw will name it based on the input file
tree_file = os.path.splitext(input_file)[0] + ".dnd"
assert os.path.isfile(tree_file), \
"Did not find tree file %s" % tree_file
os.remove(tree_file)
#Clean up any stray temp files..
if os.path.isfile("Fasta/f001.aln"):
os.remove("Fasta/f001.aln")
if os.path.isfile("Medline/pubmed_result1.aln"):
os.remove("Medline/pubmed_result1.aln")
if os.path.isfile(temp_filename_with_spaces):
os.remove(temp_filename_with_spaces)
if os.path.isfile(temp_large_fasta_file):
os.remove(temp_large_fasta_file)
print "Done"
|