def extensions_onto_foundation(otu_file_fh, extension_taxonomy_fh,
extension_seq_fh, foundation_alignment_fh,
ghost_tree_fp):
"""Combines two genetic databases into one phylogenetic tree.
Some genetic databases provide finer taxonomic resolution,
but high sequence variability causes poor multiple sequence alignments
(these are the "extension trees"). Other databases provide high quality
phylogenetic information (hence it is used as the "foundation"), but poor
taxonomic resolution. This script combines two genetic databases into
one phylogenetic tree in .nwk format, taking advantage of the benefits
of both databases, but allowing sequencing to be performed using the
"extension trees" primer set.
Parameters
__________
otu_file_fh : filehandle
Tab-delimited text file containing OTU clusters in rows containing
accession numbers only. Format can be 1) where the accession number
is in the first column with only one column or 2) it can contain
accession numbers clustered in tab-delimited rows containing more
accession numbers, which are part of that OTU cluster (as in output of
"ghost-tree group-extensions"). This file refers to the "extension
trees". File references to sequence reads or sample numbers/names are
not valid here. This is not an OTU .biom table.
extension_taxonomy_fh : filehandle
Tab-delimited text file related to "extension trees" wih the 1st
column being an
accession number (same accession numbers in otu_file_fh and
extension_taxonomy_fh) and the 2nd column is the taxonomy ranking in
the following format:
k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Sebacinales;
f__Sebacinaceae;g__unidentified;s__Sebacina
extension_seq_fh : filehandle
The .fasta formated sequences for the "extension trees" genetic
dataset. Sequence identifiers are the accession numbers. These
accession numbers are the same as in the otu_file_fh and
extension_taxonomy_fh.
foundation_alignment_fh : filehandle
File containing pre-aligned sequences from a genetic marker database
in .fasta format. This file refers to the "foundation" of the
ghost-tree. Contains accession numbers and taxonomy labels.
ghost_tree_fp : folder
Output folder contains files including:
a) The Newick formatted ghost-tree, which is the final output of the
ghost-tree tool. This is a phylogenetic tree designed for
downstream diversity analyses.
b) Accession IDs from the ghost-tree.nwk file that you can use for
downstream analyses tools
c) log error file (this is an optional file that you can have if you
type '--stderr')
"""
global foundation_accession_genus_dic # needs global assignment for flake8
foundation_accession_genus_dic = {}
std_output, std_error = "", ""
process = subprocess.Popen("muscle",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
std_output, std_error = process.communicate()
if re.search("command not found", std_error):
print "muscle, multiple sequence aligner, is not found. Is it" \
" installed? Is it in your path?"
process = subprocess.Popen("fasttree",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
std_output, std_error = process.communicate()
std_output, std_error = "", ""
if re.search("command not found", std_error):
print "fasttree, phylogenetic tree builder, is not found. Is it" \
" installed? Is it in your path?"
os.mkdir("tmp")
os.mkdir(ghost_tree_fp)
extension_genus_accession_list_dic = \
_extension_genus_accession_dic(otu_file_fh,
extension_taxonomy_fh)
skbio.write(_make_nr_foundation_alignment(
foundation_alignment_fh, extension_genus_accession_list_dic),
into=ghost_tree_fp + "/nr_foundation_alignment_gt.fasta",
format="fasta")
foundation_tree, all_std_error = _make_foundation_tree(
ghost_tree_fp + "/nr_foundation_alignment_gt.fasta", std_error,
ghost_tree_fp)
seqs = SequenceCollection.read(extension_seq_fh)
for node in foundation_tree.tips():
key_node, _ = str(node).split(":")
key_node = foundation_accession_genus_dic[key_node]
try:
_make_mini_otu_files(key_node, extension_genus_accession_list_dic,
seqs)
process = subprocess.Popen(
"muscle -in tmp/mini_seq_gt.fasta" + " -out" +
" tmp/mini_alignment_gt.fasta -quiet" + " -maxiters 2 -diags1",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
std_output, std_error = process.communicate()
process = subprocess.Popen("fasttree -nt -quiet" +
" tmp/mini_alignment_gt.fasta >" +
" tmp/mini_tree_gt.nwk",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
std_output, std_error = process.communicate()
all_std_error += "FastTree warnings for genus " + key_node + " are:\n" + std_error + "\n"
mini_tree = read("tmp/mini_tree_gt.nwk",
format='newick',
into=TreeNode)
node.extend(mini_tree.root_at_midpoint().children[:])
except:
continue
shutil.rmtree("tmp")
ghost_tree_nwk = open(ghost_tree_fp + "/ghost_tree.nwk", "w")
ghost_tree_nwk.write(str(foundation_tree))
ghost_tree_nwk.close()
_make_accession_id_file(ghost_tree_fp)
return str(foundation_tree).strip(), all_std_error
def scaffold_extensions_into_foundation(otu_file_fh, extension_taxonomy_fh,
extension_seq_fh,
foundation_alignment_fh,
ghost_tree_fp):
"""Combines two genetic databases into one phylogenetic tree.
Some genetic databases provide finer taxonomic resolution,
but high sequence variability causes poor multiple sequence alignments
(these are the "extension trees"). Other databases provide high quality
phylogenetic information (hence it is used as the "foundation"), but poor
taxonomic resolution. This script combines two genetic databases into
one phylogenetic tree in .nwk format, taking advantage of the benefits
of both databases, but allowing sequencing to be performed using the
"extension trees" primer set.
Parameters
__________
otu_file_fh : filehandle
Tab-delimited text file containing OTU clusters in rows containing
accession numbers only. Format can be 1) where the accession number
is in the first column with only one column or 2) it can contain
accession numbers clustered in tab-delimited rows containing more
accession numbers, which are part of that OTU cluster (as in output of
"ghost-tree group-extensions"). This file refers to the "extension
trees". File references to sequence reads or sample numbers/names are
not valid here. This is not an OTU .biom table.
extension_taxonomy_fh : filehandle
Tab-delimited text file related to "extension trees" wih the 1st
column being an
accession number (same accession numbers in otu_file_fh and
extension_taxonomy_fh) and the 2nd column is the taxonomy ranking in
the following format:
k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Sebacinales;
f__Sebacinaceae;g__unidentified;s__Sebacina
extension_seq_fh : filehandle
The .fasta formated sequences for the "extension trees" genetic
dataset. Sequence identifiers are the accession numbers. These
accession numbers are the same as in the otu_file_fh and
extension_taxonomy_fh.
foundation_alignment_fh : filehandle
File containing pre-aligned sequences from a genetic marker database
in .fasta format. This file refers to the "foundation" of the
ghost-tree. Contains accession numbers and taxonomy labels.
ghost_tree_fh : filehandle
The Newick formatted ghost-tree is the final output of the ghost-tree
tool. This is a phylogenetic tree designed for downstream diversity
analyses.
"""
os.system("mkdir tmp")
global foundation_accession_genus_dic
foundation_accession_genus_dic = {}
global seqs
extension_genus_accession_list_dic = \
_extension_genus_accession_dic(otu_file_fh,
extension_taxonomy_fh)
skbio.write(_make_nr_foundation_alignment(
foundation_alignment_fh, extension_genus_accession_list_dic),
into="nr_foundation_alignment_gt.fasta",
format="fasta")
foundation_tree = _make_foundation_tree("nr_foundation_alignment_gt.fasta")
seqs = SequenceCollection.read(extension_seq_fh)
for node in foundation_tree.tips():
key_node, _ = str(node).split(":")
key_node = foundation_accession_genus_dic[key_node]
try:
_make_mini_otu_files(key_node, extension_genus_accession_list_dic,
seqs)
os.system("muscle -in tmp/mini_seq_gt.fasta -out" +
" tmp/mini_alignment_gt.fasta -quiet" +
" -maxiters 2 -diags1")
os.system("fasttree -nt -quiet tmp/mini_alignment_gt.fasta >" +
" tmp/mini_tree_gt.nwk")
mini_tree = read("tmp/mini_tree_gt.nwk",
format='newick',
into=TreeNode)
node.extend(mini_tree.children[:])
except:
continue
os.system("rm -r tmp")
ghost_tree_fp.write(str(foundation_tree))
return str(foundation_tree).strip()
def scaffold_extensions_into_foundation(otu_file_fh, extension_taxonomy_fh,
extension_seq_fh,
foundation_alignment_fh,
ghost_tree_fp):
"""Combines two genetic databases into one phylogenetic tree.
Some genetic databases provide finer taxonomic resolution,
but high sequence variability causes poor multiple sequence alignments
(these are the "extension trees"). Other databases provide high quality
phylogenetic information (hence it is used as the "foundation"), but poor
taxonomic resolution. This script combines two genetic databases into
one phylogenetic tree in .nwk format, taking advantage of the benefits
of both databases, but allowing sequencing to be performed using the
"extension trees" primer set.
Parameters
__________
otu_file_fh : filehandle
Tab-delimited text file containing OTU clusters in rows containing
accession numbers only. Format can be 1) where the accession number
is in the first column with only one column or 2) it can contain
accession numbers clustered in tab-delimited rows containing more
accession numbers, which are part of that OTU cluster (as in output of
"ghost-tree group-extensions"). This file refers to the "extension
trees". File references to sequence reads or sample numbers/names are
not valid here. This is not an OTU .biom table.
extension_taxonomy_fh : filehandle
Tab-delimited text file related to "extension trees" wih the 1st
column being an
accession number (same accession numbers in otu_file_fh and
extension_taxonomy_fh) and the 2nd column is the taxonomy ranking in
the following format:
k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Sebacinales;
f__Sebacinaceae;g__unidentified;s__Sebacina
extension_seq_fh : filehandle
The .fasta formated sequences for the "extension trees" genetic
dataset. Sequence identifiers are the accession numbers. These
accession numbers are the same as in the otu_file_fh and
extension_taxonomy_fh.
foundation_alignment_fh : filehandle
File containing pre-aligned sequences from a genetic marker database
in .fasta format. This file refers to the "foundation" of the
ghost-tree. Contains accession numbers and taxonomy labels.
ghost_tree_fh : filehandle
The Newick formatted ghost-tree is the final output of the ghost-tree
tool. This is a phylogenetic tree designed for downstream diversity
analyses.
"""
global foundation_accession_genus_dic # needs global assignment for flake8
foundation_accession_genus_dic = {}
ghost_tree_output = str(ghost_tree_fp)
ghost_tree_output = ghost_tree_output[16:-4]
process = subprocess.Popen("muscle", shell=True, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
if re.search("command not found", error):
print "muscle, multiple sequence aligner, is not found. Is it" \
" installed? Is it in your path?"
process = subprocess.Popen("fasttree", shell=True, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
if re.search("command not found", error):
print "fasttree, phylogenetic tree builder, is not found. Is it" \
" installed? Is it in your path?"
os.mkdir("tmp")
logfile = open("ghost-tree_log_"+ghost_tree_output+".txt", "w")
extension_genus_accession_list_dic = \
_extension_genus_accession_dic(otu_file_fh,
extension_taxonomy_fh)
skbio.write(_make_nr_foundation_alignment(foundation_alignment_fh,
extension_genus_accession_list_dic),
into="nr_foundation_alignment_gt.fasta",
format="fasta")
foundation_tree = _make_foundation_tree("nr_foundation_alignment_gt.fasta",
logfile)
seqs = SequenceCollection.read(extension_seq_fh)
for node in foundation_tree.tips():
key_node, _ = str(node).split(":")
key_node = foundation_accession_genus_dic[key_node]
try:
_make_mini_otu_files(key_node, extension_genus_accession_list_dic,
seqs)
process = subprocess.Popen("muscle -in tmp/mini_seq_gt.fasta" +
" -out" +
" tmp/mini_alignment_gt.fasta -quiet" +
" -maxiters 2 -diags1", shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
process = subprocess.Popen("fasttree -nt -quiet" +
" tmp/mini_alignment_gt.fasta >" +
" tmp/mini_tree_gt.nwk", shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = process.communicate()
logfile.write("FastTree warnings for genus "+key_node+" are:\n" +
error + "\n")
mini_tree = read("tmp/mini_tree_gt.nwk", format='newick',
into=TreeNode)
node.extend(mini_tree.root_at_midpoint().children[:])
except:
continue
shutil.rmtree("tmp")
ghost_tree_fp.write(str(foundation_tree))
logfile.close()
return str(foundation_tree).strip()
