def constructTree(alignmentFile, treeFile, logFile, nucleotide=False):
"""
Constructs a phylogenetic tree using FastTree
"""
if nucleotide:
fastTreeCline = FastTreeCommandline(input=alignmentFile,
log=logFile,
out=treeFile,
nt=True,
gtr=True)
else:
fastTreeCline = FastTreeCommandline(input=alignmentFile,
log=logFile,
out=treeFile)
fastTreeCline()
def test_single(self):
path = "Fasta/f001"
records = list(SeqIO.parse(path, "fasta"))
self.assertEqual(len(records), 1)
cline = FastTreeCommandline(fasttree_exe, input=path)
stdout, stderr = cline()
self.assertIn("Unique: 1/1", stderr)
def fast_tree(file):
try:
FastTreeCommandline(
"fasttreemp",
nt=True,
gtr=True,
input=file,
out=f"{file}.tre",
fastest=True,
)()
except Bio.Application.ApplicationError:
FastTreeCommandline(
"fasttree",
nt=True,
gtr=True,
input=file,
out=f"{file}.tre",
fastest=True,
)()
def test_empty(self):
path = "does_not_exist.fasta"
cline = FastTreeCommandline(fasttree_exe, input=path)
with self.assertRaises(ApplicationError) as cm:
stdout, stderr = cline()
message = str(cm.exception)
self.assertTrue("Cannot open sequence file" in message
or "Cannot open sequence file" in message
or "Cannot read %s" % path in message
or "Non-zero return code " in message,
msg="Unknown ApplicationError raised: %s" % message)
def test_invalid(self):
path = "Medline/pubmed_result1.txt"
cline = FastTreeCommandline(fasttree_exe, input=path)
with self.assertRaises(ApplicationError) as cm:
stdout, stderr = cline()
message = str(cm.exception)
self.assertTrue("invalid format" in message
or "not produced" in message
or "No sequences in file" in message
or "Error parsing header line:" in message
or "Non-zero return code " in message,
msg="Unknown ApplicationError raised: %s" % message)
break
if not fasttree_exe:
raise MissingExternalDependencyError(
"Install FastTree and correctly set the file path to the program "
"if you want to use it from Biopython.")
#################################################################
print("Checking error conditions")
print("=========================")
print("Empty file")
input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = FastTreeCommandline(fasttree_exe, input=input_file)
try:
stdout, stderr = cline()
assert False, "Should have failed, returned:\n%s\n%s" % (stdout, stderr)
except ApplicationError as 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)
from Bio import AlignIO
align = AlignIO.read(child.stdout, "clustal")
print(align)
# convert into PHYLIP format
phylip = "seqs.phy"
with open(phylip, 'w') as out:
AlignIO.write(align, out, 'phylip')
###
# reconstruct phylogenetic tree
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline, FastTreeCommandline
#cmd = PhymlCommandline(input=phylip, datatype='aa')
cmd = FastTreeCommandline(input=phylip, out=phylip + ".nw")
out_log, err_log = cmd()
tree = Phylo.read(phylip + ".nw", 'newick') # '_phyml_tree.txt'
Phylo.draw_ascii(tree)
# ete
import ete3
t = ete3.PhyloTree(phylip + ".nw")
# root by mid-point
t.set_outgroup(t.get_midpoint_outgroup())
print(t)
t.show()