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# 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),
("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(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"
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