def pick_otu(spe_out, alignment):
fin = open(spe_out)
lines = fin.readlines()
fin.close()
fout = open(alignment + ".otu", "w")
aln = SeqGroup(sequences=alignment)
for i in range(len(lines)):
line = lines[i]
if line.startswith("Species"):
nline = lines[i + 1].strip()
seq = aln.get_seq(nline)
fout.write(">" + nline + "\n")
fout.write(seq + "\n")
fout.close()
def _create_tree (tree,fasta,out,color):
seqs = SeqGroup(fasta, format="fasta")
t = Tree(tree)
colors = _parse_color_file(color)
node_names = t.get_leaf_names()
for name in node_names:
seq = seqs.get_seq(name)
seqFace = SeqMotifFace(seq, seq_format="()")
node = t.get_leaves_by_name(name)
for i in range(0,len(node)):
if name in colors:
ns = NodeStyle()
ns['bgcolor'] = colors[name]
node[i].set_style(ns)
node[i].add_face(seqFace,0,'aligned')
t.render(out)
def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence",alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves)>0:
print("Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves), file=sys.stderr)
def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence", alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves) > 0:
print("Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves), file=sys.stderr)
t = PhyloTree( tree_input , format=1, quoted_node_names=True )
seqs = SeqGroup(alg, format="fasta")
nodestyle1 = NodeStyle()
nodestyle1["size"] = 0
nodestyle1["vt_line_width"] = 2
nodestyle1["hz_line_width"] = 2
for node in t.traverse():
node.set_style(nodestyle1)
for leaf in t.iter_leaves():
item=seqs.get_seq(leaf.name)
name_face = AttrFace(item, fsize=24)
Bars = SequenceFace(item, seqtype='aa', fsize=24, bg_colors={'G': 'Khaki', 'A': 'Khaki', 'S': 'Khaki', 'T': 'Khaki', 'C': 'LightGreen', 'V': 'LightGreen', 'I': 'LightGreen', 'L': 'LightGreen', 'P': 'LightGreen', 'F': 'LightGreen', 'Y': 'LightGreen', 'M': 'YellowGreen', 'W': 'LightGreen', 'N': 'Thistle', 'Q': 'Thistle', 'H': 'Thistle', 'D': 'DarkSalmon', 'E': 'DarkSalmon', 'K': 'SkyBlue', 'R': 'SkyBlue', 'X':'Black', '-':'White' }, fg_colors=None, codon=None, col_w=1.5, alt_col_w=3, special_col=None, interactive=False)
leaf.add_face(Bars, 2, "aligned")
t.render("tree_and_alignment.png", h=100, units="mm")
t.render("tree_and_alignment.svg", h=100, units="mm")
t2 = PhyloTree( tree_input , format=1, quoted_node_names=True )
for node in t2.traverse():
node.set_style(nodestyle1)
t2.convert_to_ultrametric(tree_length=None, strategy='balanced')
cf = CircleFace(10, "black")
elif ies == '0':
cf = CircleFace(10, "LightGrey")
else:
sys.exit(1)
column = hiesL[(geneFamily, homIES)] + 1
leaf.add_face(cf, column, "aligned")
drawTree(outputFile)
elif plotStyle == '3': # plot with MSA
# load nucleotide sequences for all genes!
nuclAlnFile = os.path.join(basePath, 'analysis', 'msas', 'filtered', 'cluster.' + geneFamily + '.nucl.fa')
seqs = SeqGroup(sequences = nuclAlnFile, format = "fasta")
for leaf in t:
geneId = leaf.name
seq = seqs.get_seq(geneId)
seq = seq.translate(None, string.ascii_lowercase) # keep only CDS
iesmotif = [[1, len(seq), "line", 2, 5, None, None, None]]
for homIES in gfhomIES[geneFamily]:
(begin, end, ies, iesId, beginMSA, endMSA) = charMat[(geneFamily, homIES, geneId)]
if ies == '?':
if beginMSA == 'NA':
iesmotif.append([int(begin), int(end),"()", 10, 10, "red", "black", "arial|8|black|?"])
else:
iesmotif.append([int(begin), int(end),"()", 10, 10, "red", "black", "arial|8|black|?"])
elif ies == '1':
iesmotif.append([int(beginMSA), int(endMSA),"[]", 10, 10, "black", "red", "arial|8|black|" + iesId])
elif ies == '0':
iesmotif.append([int(begin), int(end), "[]", 10, 10, "silver", "silver", None])
else:
quit(1)
import re
from ete3 import SeqGroup, Tree
import sys
alg_file = sys.argv[1] # in fasta format
tree_file = sys.argv[2] # in newick format
alg = SeqGroup(alg_file)
for k, v in alg.name2id.items():
# converts ilegal newick chars from alg names.
# Comment this line if not necessary
k = re.sub('[:,();]', '_', k)
alg.name2id[k] = v
tree = Tree(tree_file)
for leaf in tree:
print(">%s\n%s" % (leaf.name, alg.get_seq(leaf.name)))
from ete3 import SeqGroup
sp_mem = {}
in_fasta = SeqGroup('/home/plaza/research/dom_walk/raw/COG0484.faa')
for num, (name, seq, _) in enumerate(in_fasta):
sp = name.split('.')[0]
if sp not in sp_mem:
sp_mem[sp] = []
sp_mem[sp].append(name)
print ('writing fastas per sp')
for k, val in sp_mem.items():
out_fasta = open('/home/plaza/research/dom_walk/analysis/fasta_per_sp/'+k+'.faa', 'w')
for seq_name in val:
print (">%s" %(seq_name), file = out_fasta)
print (in_fasta.get_seq(seq_name), file =out_fasta)
out_fasta.close()
from ete3 import SeqGroup, Tree
import sys
tree_file = sys.argv[1] # in newick format
original_fasta = SeqGroup(sys.argv[2])
pruned_fasta = open(sys.argv[3], 'w')
star_target = str(sys.argv[4])
end_target = str(sys.argv[5])
tree = Tree(tree_file)
R = tree.get_midpoint_outgroup()
tree.set_outgroup(R)
name_list = []
for num, leaf in enumerate(tree):
name_list.append(leaf.name)
if star_target == leaf.name:
star_pos = num
if end_target == leaf.name:
end_pos = num
pruned_list = name_list[star_pos:(end_pos + 1)]
print pruned_list
#for ele in pruned_list:
# print >>pruned_fasta,">%s\n%s"%(ele, original_fasta.get_seq(ele))
for ele in name_list:
if ele not in pruned_list:
print >> pruned_fasta, ">%s\n%s" % (ele, original_fasta.get_seq(ele))
