def add(file, family_key):
with open(file) as handle:
from Bio.Nexus.Trees import Tree as NexusTree
tree = NexusTree(handle.read())
dbtree = Tree()
dbtree.family_key = family_key
dbtree.text = tree.to_string(plain=False, plain_newick=True)
dbtree.filename = os.path.basename(file)
session.add(dbtree)
session.flush()
tree.name = dbtree.id
for node in TreeNodeFactory().create(tree):
session.add(node)
def add(file, family_key):
with open(file) as handle:
from Bio.Nexus.Trees import Tree as NexusTree
tree = NexusTree(handle.read())
dbtree = Tree()
dbtree.family_key = family_key
dbtree.text = tree.to_string(plain=False,plain_newick=True)
dbtree.filename = os.path.basename(file)
session.add(dbtree)
session.flush()
tree.name = dbtree.id
for node in TreeNodeFactory().create(tree):
session.add(node)
class OIDImporter(object):
"""
Import a set of OID files into the database
"""
def __init__(
self,
familyName,
alignFile,
alignColcullLog,
alignSeqcullLog,
treeFile,
treeDiagCharsFile,
codemlFile=None,
alignFormat="fasta",
oid_key=None,
):
self.familyName = familyName
self.treeFile = treeFile
self.treeDiagCharsFile = treeDiagCharsFile
self.alignFile = alignFile
self.alignColcullLog = alignColcullLog
self.alignSeqcullLog = alignSeqcullLog
self.codemlFile = codemlFile
self.alignFormat = alignFormat
self.oid_key = oid_key
def merge(self):
from hpf.hddb.db import Session, Family
self.session = Session()
self.family = self.session.query(Family).filter(Family.name == self.familyName).first()
if not self.family:
runtime().debug("Creating family", self.familyName)
self._family()
self._alignment()
self._tree()
else:
self.alignment = self.family.alignment
self.tree = self.alignment.tree
runtime().debug("Found family", self.family.id)
if not self.family.alignments[0].tree.codeml:
runtime().debug("Importing codeml")
self._codeml()
else:
runtime().debug("Already found codeml", self.family.alignments[0].tree.codeml.id)
# Commit the session, close, and finish
self.session.commit()
self.session.close()
def _index(self, name):
n = name.split("#")[-1]
if n.startswith("N"):
n = n[1:]
assert n.isdigit()
return n
def _tree(self):
session = self.session
# # Load the tree file and rename the taxa.
# from Bio.Nexus.Nexus import Nexus
# nex=Nexus(self.treeFile)
# self.nexus = nex.trees[0]
from Bio.Nexus.Trees import Tree as NewickTree
tree_str = open(self.treeFile).read()
self.nexus = NewickTree(tree_str)
# Rename all the taxa.
for id in self.nexus.get_terminals():
node = self.nexus.node(id)
node.data.taxon = self._index(node.data.taxon)
# Create the DB object
from hpf.hddb.db import Tree
self.tree = Tree(
alignment_key=self.alignment.id,
text=self.nexus.to_string(plain=False, plain_newick=True),
filename=self.treeFile,
)
session.add(self.tree)
session.flush()
# Now add in the node references
self.nexus.name = self.tree.id
assert self.tree.id != None
runtime().debug("Added tree", self.tree)
from hpf.hddb.db import TreeNodeFactory
nodes = list(TreeNodeFactory().create(self.nexus))
for node in nodes:
node.ancestor_node = node.ancestor.id if node.ancestor else None
# This should add the new object into the session
self.tree.nodes.append(node)
# session.add(node)
session.flush()
runtime().debug("Appended", len(nodes), "tree nodes")
session.flush()
# Now import the diagnostic characters and reference the nodes.
from hpf.amnh.oid import DiagCharsParser
from hpf.hddb.db import TreeFactory
biotree = TreeFactory(name_func=lambda node: str(node.id)).create(self.tree.nodes, self.tree.id)
parser = DiagCharsParser(biotree)
runtime().debug(self.treeDiagCharsFile)
with open(self.treeDiagCharsFile) as handle:
diagchars = list(parser.parse(handle))
runtime().debug("DiagChars", len(diagchars))
for d in diagchars:
session.add(d)
session.flush()
def _codeml(self):
if not self.codemlFile:
return
assert self.family.id != None
assert self.tree.id != None
# We need to convert the columns to the original alignment indices
mapper = CulledColumnMapper(self.alignment, self.alignment.culled_columns)
parser = PositiveSelectionParser()
models = list(parser.parse(self.codemlFile))
runtime().debug("Found", len(models), "models")
for i, model in enumerate(models):
model.tree_key = self.tree.id
self.session.add(model)
self.session.flush()
ps = list(model.ps)
runtime().debug("Found", len(ps), "sites in model", model.model)
for j, site in enumerate(ps):
site.codeml_key = model.id
# Indices in CodeML start at 1, convert to 0 and then map
orig = site.column
site.column = mapper[site.column - 1]
runtime().debug("column", orig, "mapped to", site.column, site.probability)
try:
self.session.add(site)
except:
runtime().debug(i, ":", j, " failure on column", orig, "mapped to", site.column, site.probability)
raise
runtime().debug("Finished with model")
self.session.flush()
# with open(self.codemlFile) as handle:
# text = handle.read()
# from hpf.hddb.db import CodeML
# self.codeml = CodeML(tree_key=self.tree.id,
# filename=self.codemlFile,
# text=text)
# self.session.add(self.codeml)
# self.session.flush()
# parser = LRTParser(self.alignment, self.alignment.culled_columns,self.codeml)
# with open(self.codemlFile) as handle:
# for selection in parser.parse(handle):
# selection.codeml_key = self.codeml.id
# self.session.merge(selection)
runtime().debug("finished import codeml")
def _alignment(self):
session = self.session
# Read the alignment
from Bio import AlignIO
with open(self.alignFile) as handle:
align = AlignIO.read(handle, self.alignFormat)
# Rename 'id' with the correct protein key
for record in align:
record.id = self._index(record.id)
# Write to a text buffer and create the DB object
text = StringIO()
AlignIO.write([align], text, self.alignFormat)
from hpf.hddb.db import Alignment
self.alignment = Alignment(
family_key=self.family.id, format=self.alignFormat, filename=self.alignFile, text=text.getvalue()
)
# Add to session and flush
session.add(self.alignment)
session.flush()
# Flip through the proteins in the alignment and add
# the records.
for record in align:
protein_key = record.id
assert protein_key != 0 and protein_key != None, protein_key
runtime().debug("protein: ", protein_key)
from hpf.hddb.db import AlignmentProtein
s = AlignmentProtein(alignment_key=self.alignment.id, protein_key=protein_key, sequence=str(record.seq))
session.add(s)
session.flush()
# There may exist multiple alignments, but the definition
# of membership in the family is done here.
from hpf.hddb.db import FamilyProtein
fs = FamilyProtein(family_key=self.family.id, protein_key=protein_key, seed=True)
session.merge(fs)
# Now read the colulmn culling log. Indices start at 0 here.
from hpf.hddb.db import AlignmentColcull, AlignmentSeqcull
with open(self.alignColcullLog) as handle:
for line in handle:
column, gap, taxa, ratio = line.split()
col = AlignmentColcull(alignment_key=self.alignment.id, column=column, gap_percentage=ratio)
session.merge(col)
with open(self.alignSeqcullLog) as handle:
# rice#1182215 0.712765957446808
for line in handle:
parts = line.split()
seq, score = parts
seq = self._index(seq)
# seq.split("#")[-1]
if not seq.isdigit():
print parts, "SEQ:", seq
assert false
cul = AlignmentSeqcull(alignment_key=self.alignment.id, protein_key=seq, score=score)
session.flush()
def _family(self):
session = self.session
from hpf.hddb.db import Family
self.family = Family(name=self.familyName, experiment_key=0)
session.add(self.family)
session.flush()
else:
badtaxa.append(taxon)
else:
slowest_inparalogs[sp] = (taxon,
mytreeobj.node(
mytreeobj.search_taxon(taxon)
).get_data().branchlength)
for taxon in badtaxa:
mytreeobj.prune(taxon)
### print tree file ###
treestr = mytreeobj.to_string(branchlengths_only=True,
plain_newick=True)
outfname = '%s/%d.tre' % (resultdir, phogacc)
outf = open(outfname, 'w')
print >> outf, treestr
outf.close()
### now get the alignment ###
alnfname = dirbase + bpg[0:6] + '/' + bpg[0:9] + '/user/shmms/' + bpg[
0:9] + '.subfam'
outfname = '%s/%d.a2m' % (resultdir, phogacc)
outfile = open(outfname, 'w')
handle = open(alnfname, 'r')
doneit = set([])
class OIDImporter(object):
"""
Import a set of OID files into the database
"""
def __init__(self,
familyName,
alignFile,
alignColcullLog,
alignSeqcullLog,
treeFile,
treeDiagCharsFile,
codemlFile=None,
alignFormat="fasta",
oid_key=None):
self.familyName = familyName
self.treeFile = treeFile
self.treeDiagCharsFile = treeDiagCharsFile
self.alignFile = alignFile
self.alignColcullLog = alignColcullLog
self.alignSeqcullLog = alignSeqcullLog
self.codemlFile = codemlFile
self.alignFormat = alignFormat
self.oid_key = oid_key
def merge(self):
from hpf.hddb.db import Session, Family
self.session = Session()
self.family = self.session.query(Family).filter(
Family.name == self.familyName).first()
if not self.family:
runtime().debug("Creating family", self.familyName)
self._family()
self._alignment()
self._tree()
else:
self.alignment = self.family.alignment
self.tree = self.alignment.tree
runtime().debug("Found family", self.family.id)
if not self.family.alignments[0].tree.codeml:
runtime().debug("Importing codeml")
self._codeml()
else:
runtime().debug("Already found codeml",
self.family.alignments[0].tree.codeml.id)
# Commit the session, close, and finish
self.session.commit()
self.session.close()
def _index(self, name):
n = name.split("#")[-1]
if n.startswith("N"):
n = n[1:]
assert n.isdigit()
return n
def _tree(self):
session = self.session
# # Load the tree file and rename the taxa.
# from Bio.Nexus.Nexus import Nexus
# nex=Nexus(self.treeFile)
# self.nexus = nex.trees[0]
from Bio.Nexus.Trees import Tree as NewickTree
tree_str = open(self.treeFile).read()
self.nexus = NewickTree(tree_str)
# Rename all the taxa.
for id in self.nexus.get_terminals():
node = self.nexus.node(id)
node.data.taxon = self._index(node.data.taxon)
# Create the DB object
from hpf.hddb.db import Tree
self.tree = Tree(alignment_key=self.alignment.id,
text=self.nexus.to_string(plain=False,
plain_newick=True),
filename=self.treeFile)
session.add(self.tree)
session.flush()
# Now add in the node references
self.nexus.name = self.tree.id
assert self.tree.id != None
runtime().debug("Added tree", self.tree)
from hpf.hddb.db import TreeNodeFactory
nodes = list(TreeNodeFactory().create(self.nexus))
for node in nodes:
node.ancestor_node = node.ancestor.id if node.ancestor else None
# This should add the new object into the session
self.tree.nodes.append(node)
#session.add(node)
session.flush()
runtime().debug("Appended", len(nodes), "tree nodes")
session.flush()
# Now import the diagnostic characters and reference the nodes.
from hpf.amnh.oid import DiagCharsParser
from hpf.hddb.db import TreeFactory
biotree = TreeFactory(name_func=lambda node: str(node.id)).create(
self.tree.nodes, self.tree.id)
parser = DiagCharsParser(biotree)
runtime().debug(self.treeDiagCharsFile)
with open(self.treeDiagCharsFile) as handle:
diagchars = list(parser.parse(handle))
runtime().debug("DiagChars", len(diagchars))
for d in diagchars:
session.add(d)
session.flush()
def _codeml(self):
if not self.codemlFile:
return
assert self.family.id != None
assert self.tree.id != None
# We need to convert the columns to the original alignment indices
mapper = CulledColumnMapper(self.alignment,
self.alignment.culled_columns)
parser = PositiveSelectionParser()
models = list(parser.parse(self.codemlFile))
runtime().debug("Found", len(models), "models")
for i, model in enumerate(models):
model.tree_key = self.tree.id
self.session.add(model)
self.session.flush()
ps = list(model.ps)
runtime().debug("Found", len(ps), "sites in model", model.model)
for j, site in enumerate(ps):
site.codeml_key = model.id
# Indices in CodeML start at 1, convert to 0 and then map
orig = site.column
site.column = mapper[site.column - 1]
runtime().debug("column", orig, "mapped to", site.column,
site.probability)
try:
self.session.add(site)
except:
runtime().debug(i, ":", j, " failure on column", orig,
"mapped to", site.column, site.probability)
raise
runtime().debug("Finished with model")
self.session.flush()
# with open(self.codemlFile) as handle:
# text = handle.read()
# from hpf.hddb.db import CodeML
# self.codeml = CodeML(tree_key=self.tree.id,
# filename=self.codemlFile,
# text=text)
# self.session.add(self.codeml)
# self.session.flush()
# parser = LRTParser(self.alignment, self.alignment.culled_columns,self.codeml)
# with open(self.codemlFile) as handle:
# for selection in parser.parse(handle):
# selection.codeml_key = self.codeml.id
# self.session.merge(selection)
runtime().debug("finished import codeml")
def _alignment(self):
session = self.session
# Read the alignment
from Bio import AlignIO
with open(self.alignFile) as handle:
align = AlignIO.read(handle, self.alignFormat)
# Rename 'id' with the correct protein key
for record in align:
record.id = self._index(record.id)
# Write to a text buffer and create the DB object
text = StringIO()
AlignIO.write([align], text, self.alignFormat)
from hpf.hddb.db import Alignment
self.alignment = Alignment(family_key=self.family.id,
format=self.alignFormat,
filename=self.alignFile,
text=text.getvalue())
# Add to session and flush
session.add(self.alignment)
session.flush()
# Flip through the proteins in the alignment and add
# the records.
for record in align:
protein_key = record.id
assert protein_key != 0 and protein_key != None, protein_key
runtime().debug("protein: ", protein_key)
from hpf.hddb.db import AlignmentProtein
s = AlignmentProtein(alignment_key=self.alignment.id,
protein_key=protein_key,
sequence=str(record.seq))
session.add(s)
session.flush()
# There may exist multiple alignments, but the definition
# of membership in the family is done here.
from hpf.hddb.db import FamilyProtein
fs = FamilyProtein(family_key=self.family.id,
protein_key=protein_key,
seed=True)
session.merge(fs)
# Now read the colulmn culling log. Indices start at 0 here.
from hpf.hddb.db import AlignmentColcull, AlignmentSeqcull
with open(self.alignColcullLog) as handle:
for line in handle:
column, gap, taxa, ratio = line.split()
col = AlignmentColcull(alignment_key=self.alignment.id,
column=column,
gap_percentage=ratio)
session.merge(col)
with open(self.alignSeqcullLog) as handle:
#rice#1182215 0.712765957446808
for line in handle:
parts = line.split()
seq, score = parts
seq = self._index(seq)
#seq.split("#")[-1]
if not seq.isdigit():
print parts, "SEQ:", seq
assert false
cul = AlignmentSeqcull(alignment_key=self.alignment.id,
protein_key=seq,
score=score)
session.flush()
def _family(self):
session = self.session
from hpf.hddb.db import Family
self.family = Family(name=self.familyName, experiment_key=0)
session.add(self.family)
session.flush()
