Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

176 lines (155 sloc) 6.924 kb
# Copyright 2008-2011 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.
from Bio import MissingExternalDependencyError
import sys
import os
from Bio import SeqIO
from Bio import AlignIO
from Bio.Align.Applications import ClustalOmegaCommandline
from Bio.Application import ApplicationError
#################################################################
#Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
clustalo_exe = None
if sys.platform=="win32":
#TODO
raise MissingExternalDependencyError("Testing this on Windows not implemented yet")
else:
import commands
output = commands.getoutput("clustalo --help")
if output.startswith("Clustal Omega"):
clustalo_exe = "clustalo"
if not clustalo_exe:
raise MissingExternalDependencyError(\
"Install clustalo if you want to use Clustal Omega from Biopython.")
#################################################################
print "Checking error conditions"
print "========================="
print "Empty file"
input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError, 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 \
"Cannot open input file" in str(err) or \
"non-zero exit status" in str(err), str(err)
print
print "Single sequence"
input_file = "Fasta/f001"
assert os.path.isfile(input_file)
assert len(list(SeqIO.parse(input_file,"fasta")))==1
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError, err:
print "Failed (good)"
assert "contains 1 sequence, nothing to align" in str(err), str(err)
print
print "Invalid sequence"
input_file = "Medline/pubmed_result1.txt"
assert os.path.isfile(input_file)
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError, 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 "Can't determine format of sequence file" in str(err), 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("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("NBRF/Cw_prot.pir", "pir"))[:40]
SeqIO.write(records, handle, "fasta")
handle.close()
del handle, records
for input_file, output_file, newtree_file in [
("Registry/seqs.fasta", "temp with space.aln", None),
("Registry/seqs.fasta", "temp_test.aln", None),
("Fasta/f002", "temp_test.aln", "temp_test.dnd"),
("Fasta/f002", "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(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)
#Any filesnames with spaces should get escaped with quotes automatically.
#Using keyword arguments here, force=True to over-write the output file.
cline = ClustalOmegaCommandline(clustalo_exe,
infile=input_file,
outfile=output_file,
outfmt="clustal",
force=True)
assert str(eval(repr(cline)))==str(cline)
if newtree_file is not None:
#Test using a property:
cline.guidetree_out = newtree_file
assert str(eval(repr(cline)))==str(cline)
#print cline
output, error = cline()
#assert output, "No output from: %s\n%s" % (cline, error)
assert not output or output.strip().startswith("CLUSTAL"), output
assert error.strip() == "" or \
error.startswith("WARNING: Sequence type is DNA."), error
#Check the output...
align = AlignIO.read(output_file, "clustal")
#The length of the alignment will depend on the version of clustalw
#(clustalw 2.0.10 and clustalw 1.83 are certainly different).
print "Got an alignment, %i sequences" % (len(align))
output_records = SeqIO.to_dict(SeqIO.parse(output_file,"clustal"))
assert len(set(input_records.keys())) == len(set(output_records.keys())), \
"%r vs %r" %(sorted(input_records.keys()), sorted(output_records.keys()))
#TODO - Investigate Clustal Omega underscore/semi-colon mapping
#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)
#TODO Check the DND file was created.
#TODO - Try and parse this with Bio.Nexus?
if newtree_file is not None \
and os.path.isfile(newtree_file):
os.remove(newtree_file)
#Clean up any stray temp files..
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"
Jump to Line
Something went wrong with that request. Please try again.