def show_GUI_TREE(ETETree):
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
ts.show_border = True
ETETree.show(tree_style=ts)
def plot_species_tree(tree_newick, tree_type, gene_name, tree_file_name,
name_list, tree_image_folder):
# set tree parameters
tree = Tree(tree_newick, format=2)
ts = TreeStyle()
ts.mode = "r" # tree model: 'r' for rectangular, 'c' for circular
ts.show_leaf_name = False
tree_title = tree_type + ' (' + gene_name + ')' # define tree title
# set tree title text parameters
ts.title.add_face(TextFace(tree_title,
fsize=8,
fgcolor='black',
ftype='Arial',
tight_text=False),
column=0) # tree title text setting
# set layout parameters
ts.rotation = 0 # from 0 to 360
ts.show_scale = False
ts.margin_top = 10 # top tree image margin
ts.margin_bottom = 10 # bottom tree image margin
ts.margin_left = 10 # left tree image margin
ts.margin_right = 10 # right tree image margin
ts.show_border = False # set tree image border
ts.branch_vertical_margin = 3 # 3 pixels between adjancent branches
# set tree node style
for each_node in tree.traverse():
# leaf node parameters
if each_node.is_leaf():
ns = NodeStyle()
ns['shape'] = 'circle' # dot shape: circle, square or sphere
ns['size'] = 0 # dot size
ns['hz_line_width'] = 0.5 # branch line width
ns['vt_line_width'] = 0.5 # branch line width
ns['hz_line_type'] = 0 # branch line type: 0 for solid, 1 for dashed, 2 for dotted
ns['vt_line_type'] = 0 # branch line type
if each_node.name in name_list:
ns['fgcolor'] = 'red' # the dot setting
each_node.add_face(
TextFace(each_node.name,
fsize=8,
fgcolor='red',
tight_text=False,
bold=False),
column=0,
position='branch-right') # the node name text setting
each_node.set_style(ns)
else:
ns['fgcolor'] = 'blue' # the dot setting
each_node.add_face(
TextFace(each_node.name,
fsize=8,
fgcolor='black',
tight_text=False,
bold=False),
column=0,
position='branch-right') # the node name text setting
each_node.set_style(ns)
# non-leaf node parameters
else:
nlns = NodeStyle()
nlns['size'] = 0 # dot size
each_node.add_face(
TextFace(each_node.name,
fsize=4,
fgcolor='black',
tight_text=False,
bold=False),
column=5,
position='branch-top') # non-leaf node name text setting)
each_node.set_style(nlns)
# set figures size
tree.render('%s/%s.png' % (tree_image_folder, tree_file_name),
w=900,
units='px',
tree_style=ts)
def plot_tree(tree, tree_title, tree_output):
# set tree parameters
ts = TreeStyle()
ts.mode = "r" # tree model: 'r' for rectangular, 'c' for circular
ts.show_leaf_name = 0
# set tree title text parameters
ts.title.add_face(TextFace(tree_title,
fsize=8,
fgcolor='black',
ftype='Arial',
tight_text=False),
column=0) # tree title text setting
# set layout parameters
ts.rotation = 0 # from 0 to 360
ts.show_scale = False
ts.margin_top = 10 # top tree image margin
ts.margin_bottom = 10 # bottom tree image margin
ts.margin_left = 10 # left tree image margin
ts.margin_right = 10 # right tree image margin
ts.show_border = False # set tree image border
ts.branch_vertical_margin = 3 # 3 pixels between adjancent branches
# set tree node style
for each_node in tree.traverse():
# leaf node parameters
if each_node.is_leaf():
ns = NodeStyle()
ns["shape"] = "circle" # dot shape: circle, square or sphere
ns["size"] = 0 # dot size
ns['hz_line_width'] = 0.5 # branch line width
ns['vt_line_width'] = 0.5 # branch line width
ns['hz_line_type'] = 0 # branch line type: 0 for solid, 1 for dashed, 2 for dotted
ns['vt_line_type'] = 0 # branch line type
ns["fgcolor"] = "blue" # the dot setting
each_node.add_face(TextFace(each_node.name,
fsize=5,
fgcolor='black',
tight_text=False,
bold=False),
column=0,
position='branch-right'
) # leaf node the node name text setting
each_node.set_style(ns)
# non-leaf node parameters
else:
nlns = NodeStyle()
nlns["size"] = 0 # dot size
#nlns["rotation"] = 45
each_node.add_face(
TextFace(each_node.name,
fsize=3,
fgcolor='black',
tight_text=False,
bold=False),
column=5,
position='branch-top') # non-leaf node name text setting)
each_node.set_style(nlns)
tree.render(tree_output, w=900, units="px",
tree_style=ts) # set figures size
DATA_PATH = {"northeuralex": "data/northeuralex-cldf-20210111-fix-pd.tsv",
"ielex": "data/ielex-4-26-2016.csv"}
DATA_URL = {"northeuralex": "http://www.sfs.uni-tuebingen.de/~jdellert/northeuralex/0.9/northeuralex-0.9-forms.tsv",
"ielex": "TEST"}
CLTS_PATH = "v1.4.1.tar.gz"
CLTS_URL = "https://github.com/cldf-clts/clts/archive/v1.4.1.tar.gz"
# Define tree style
ETE_TREE_STYLE = TreeStyle()
ETE_TREE_STYLE.show_scale = False
ETE_TREE_STYLE.show_leaf_name = False
ETE_TREE_STYLE.force_topology = False
ETE_TREE_STYLE.show_border = False
ETE_TREE_STYLE.margin_top = ETE_TREE_STYLE.margin_bottom = ETE_TREE_STYLE.margin_right = ETE_TREE_STYLE.margin_left = 5
ETE_NODE_STYLE = NodeStyle()
ETE_NODE_STYLE["size"] = 0 # remove balls from leaves
config = {
"n_hidden": N_HIDDEN,
"n_layers_encoder": N_LAYERS_ENCODER,
"n_layers_decoder": N_LAYERS_DECODER,
"dropout": DROPOUT,
"bidirectional_encoder": BIDIRECTIONAL_ENCODER,
"bidirectional_decoder": BIDIRECTIONAL_DECODER,
"encoder_all_steps": ENCODER_ALL_STEPS,
"batch_size": BATCH_SIZE,
"learning_rate": LEARNING_RATE,
def treeMaker(path_to_prokka, path_to_hmm, pwd_hmmsearch_exe, pwd_mafft_exe,
pwd_fasttree_exe, plot_tree):
# Tests for presence of the tmp folder and deletes it
tmp_folder = 'get_species_tree_wd'
if os.path.exists(tmp_folder):
os.system('rm -r ' + tmp_folder)
os.mkdir(tmp_folder)
# List all prokka dirs in the target folder
prokka_files = [
i for i in os.listdir(path_to_prokka)
if os.path.isdir(path_to_prokka + '/' + i)
]
print('Detected %i input genomes' % len(prokka_files))
# Running hmmsearch on each file
print('Running hmmsearch...')
for f in prokka_files:
# call hmmsearch
#os.system('hmmsearch -o /dev/null --domtblout %s/%s_hmmout.tbl %s %s/%s/%s.faa' % (tmp_folder, f, path_to_hmm, path_to_prokka, f, f))
os.system(
'%s -o /dev/null --domtblout %s/%s_hmmout.tbl %s %s/%s/%s.faa' %
(pwd_hmmsearch_exe, tmp_folder, f, path_to_hmm, path_to_prokka, f,
f))
# Reading the protein file in a dictionary
proteinSequence = {}
for seq_record in SeqIO.parse('%s/%s/%s.faa' % (path_to_prokka, f, f),
'fasta'):
proteinSequence[seq_record.id] = str(seq_record.seq)
# Reading the hmmersearch table/extracting the protein part found beu hmmsearch out of the protein/Writing each protein sequence that was extracted to a fasta file (one for each hmm in phylo.hmm
hmm_id = ''
hmm_name = ''
hmm_pos1 = 0
hmm_pos2 = 0
hmm_score = 0
with open(tmp_folder + '/' + f.replace('prokka/', '') + '_hmmout.tbl',
'r') as tbl:
for line in tbl:
if line[0] == "#": continue
line = re.sub('\s+', ' ', line)
splitLine = line.split(' ')
if (hmm_id == ''):
hmm_id = splitLine[4]
hmm_name = splitLine[0]
hmm_pos1 = int(splitLine[17]) - 1
hmm_pos2 = int(splitLine[18])
hmm_score = float(splitLine[13])
elif (hmm_id == splitLine[4]):
if (float(splitLine[13]) > hmm_score):
hmm_name = splitLine[0]
hmm_pos1 = int(splitLine[17]) - 1
hmm_pos2 = int(splitLine[18])
hmm_score = float(splitLine[13])
else:
file_out = open(tmp_folder + '/' + hmm_id + '.fasta', 'a+')
file_out.write('>' + f + '\n')
if hmm_name != '':
seq = str(proteinSequence[hmm_name][hmm_pos1:hmm_pos2])
file_out.write(str(seq) + '\n')
file_out.close()
hmm_id = splitLine[4]
hmm_name = splitLine[0]
hmm_pos1 = int(splitLine[17]) - 1
hmm_pos2 = int(splitLine[18])
hmm_score = float(splitLine[13])
else:
file_out = open(tmp_folder + '/' + hmm_id + '.fasta', 'a+')
file_out.write('>' + f + '\n')
if hmm_name != '':
seq = str(proteinSequence[hmm_name][hmm_pos1:hmm_pos2])
file_out.write(str(seq) + '\n')
file_out.close()
# Call mafft to align all single fasta files with hmms
files = os.listdir(tmp_folder)
fastaFiles = [i for i in files if i.endswith('.fasta')]
print('Running mafft...')
for f in fastaFiles:
fastaFile1 = '%s/%s' % (tmp_folder, f)
fastaFile2 = fastaFile1.replace('.fasta', '_aligned.fasta')
os.system(pwd_mafft_exe + ' --quiet --maxiterate 1000 --globalpair ' +
fastaFile1 + ' > ' + fastaFile2 + ' ; rm ' + fastaFile1)
# concatenating the single alignments
# create the dictionary
print('Concatenating alignments...')
concatAlignment = {}
for element in prokka_files:
concatAlignment[element] = ''
# Reading all single alignment files and append them to the concatenated alignment
files = os.listdir(tmp_folder)
fastaFiles = [i for i in files if i.endswith('.fasta')]
for f in fastaFiles:
fastaFile = tmp_folder + '/' + f
proteinSequence = {}
alignmentLength = 0
for seq_record_2 in SeqIO.parse(fastaFile, 'fasta'):
proteinName = seq_record_2.id
proteinSequence[proteinName] = str(seq_record_2.seq)
alignmentLength = len(proteinSequence[proteinName])
for element in prokka_files:
if element in proteinSequence.keys():
concatAlignment[element] += proteinSequence[element]
else:
concatAlignment[element] += '-' * alignmentLength
# writing alignment to file
file_out = open('./species_tree.aln', 'w')
for element in prokka_files:
file_out.write('>' + element + '\n' + concatAlignment[element] + '\n')
file_out.close()
# calling fasttree for tree calculation
print('Running fasttree...')
os.system('%s -quiet species_tree.aln > species_tree.newick' %
pwd_fasttree_exe)
# Decomment the two following lines if tree is rooted but should be unrooted
#phyloTree = dendropy.Tree.get(path='phylogenticTree.phy', schema='newick', rooting='force-unrooted')
#dendropy.Tree.write_to_path(phyloTree, 'phylogenticTree_unrooted.phy', 'newick')
# plot species tree
if plot_tree == 1:
print('Plot species tree')
tree = Tree('species_tree.newick', format=1)
# set tree parameters
ts = TreeStyle()
ts.mode = "r" # tree model: 'r' for rectangular, 'c' for circular
ts.show_leaf_name = 0
# set tree title text parameters
ts.title.add_face(TextFace('Species_Tree',
fsize=8,
fgcolor='black',
ftype='Arial',
tight_text=False),
column=0) # tree title text setting
# set layout parameters
ts.rotation = 0 # from 0 to 360
ts.show_scale = False
ts.margin_top = 10 # top tree image margin
ts.margin_bottom = 10 # bottom tree image margin
ts.margin_left = 10 # left tree image margin
ts.margin_right = 10 # right tree image margin
ts.show_border = False # set tree image border
ts.branch_vertical_margin = 3 # 3 pixels between adjancent branches
# set tree node style
for each_node in tree.traverse():
# leaf node parameters
if each_node.is_leaf():
ns = NodeStyle()
ns["shape"] = "circle" # dot shape: circle, square or sphere
ns["size"] = 0 # dot size
ns['hz_line_width'] = 0.5 # branch line width
ns['vt_line_width'] = 0.5 # branch line width
ns['hz_line_type'] = 0 # branch line type: 0 for solid, 1 for dashed, 2 for dotted
ns['vt_line_type'] = 0 # branch line type
ns["fgcolor"] = "blue" # the dot setting
each_node.add_face(TextFace(each_node.name,
fsize=5,
fgcolor='black',
tight_text=False,
bold=False),
column=0,
position='branch-right'
) # leaf node the node name text setting
each_node.set_style(ns)
# non-leaf node parameters
else:
nlns = NodeStyle()
nlns["size"] = 0 # dot size
# nlns["rotation"] = 45
each_node.add_face(
TextFace(each_node.name,
fsize=3,
fgcolor='black',
tight_text=False,
bold=False),
column=5,
position='branch-top') # non-leaf node name text setting)
each_node.set_style(nlns)
tree.render('species_tree' + '.png', w=900, units="px",
tree_style=ts) # set figures size
if plot_tree == 0:
print('The built species tree was exported to species_tree.newick')
else:
print(
'The built species tree was exported to species_tree.newick and species_tree.png'
)
