def _import_protein_details(self, ms_job):
for row in self.protein_details:
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Protein Details ({})".format(
row["ID"])
self.current += 1
self.notify_progress(current=self.current,
total=self.total,
message=outstr)
ref_protein = cmodels.MassSpectrometryProtein.objects.for_species(
self.species).for_wid(slugify(row["ID"]))
coordinate, length = map(
lambda x: int(x), row["Position (to mature prot.)"].split("-"))
cmodels.MassSpectrometryProteinDetail.objects.get_or_create_with_revision(
self.detail,
protein=ref_protein,
sequence=row["Sequence"],
sequence_ptm=row["Sequence + PTMs"],
coordinate=coordinate,
length=length - coordinate,
proteotypic=row["Proteotypic"],
zscore=row["z-score"],
delta_mass=row["Delta Mass (ppm)"],
mass=row["Experimental Mass (m/z)"],
charge=row["Charge"],
retention_time=row["Retention Time (min)"],
theoretical_mass=row["Theoretical Mass (Da)"],
missed_cleavages=row["Missed Cleavages"])
def handle(self, *args, **options):
if not options["wid"]:
raise CommandError("wid argument is mandatory")
if not options["reason"]:
raise CommandError("reason is mandatory")
wid = slugify(options["wid"])
reason = options["reason"]
if options["wid"] != wid:
raise CommandError(
"Wid {} contained invalid characters. Only letters, numbers and _ are allowed"
.format(options["wid"]))
try:
species_obj = Species.objects.get(wid=wid)
except:
if self.verify_species_exists:
raise CommandError("Species {} not found".format(wid))
else:
species_obj = Species(wid=wid)
if not options["user"]:
options["user"] = "******"
revdetail = RevisionDetail()
revdetail.user = UserProfile.objects.get(
user__username=options["user"])
revdetail.reason = reason
revdetail.save()
self.handle_command(species_obj, revdetail, *args, **options)
def _import_target_peptides(self, ms_job):
target_type = cmodels.Type.objects.for_wid("Target-Peptide",
create=True)
target_type.species = self.species
target_type.save(self.detail)
for i, item in enumerate(self.target_peptides):
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Target Peptide ({})".format(
item["Matched Proteins"])
self.current += 1
self.notify_progress(current=self.current,
total=self.total,
message=outstr)
peptide = cmodels.Peptide.objects.for_species(
self.species).for_wid("{}-{}".format(
i + 1, slugify(item["Matched Proteins"])),
create=True)
peptide.parent = ms_job
peptide.sequence = item["Sequence"]
peptide.length = len(item["Sequence"])
peptide.proteotypic = item["Proteotypic"]
peptide.charge = item["Charge"]
peptide.mass = item["m/z"]
peptide.zscore = item["zscore"]
peptide.retention_time = item["RT"]
peptide.species = self.species
peptide.save(self.detail)
peptide.type.add(target_type)
for protein in item["Matched Proteins"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(
self.detail, value=protein.strip())
peptide.proteins.add(prot)
def handle(self, *args, **options):
if not options["wid"]:
raise CommandError("wid argument is mandatory")
if not options["reason"]:
raise CommandError("reason is mandatory")
wid = slugify(options["wid"])
reason = options["reason"]
if options["wid"] != wid:
raise CommandError("Wid {} contained invalid characters. Only letters, numbers and _ are allowed".format(options["wid"]))
try:
species_obj = Species.objects.get(wid = wid)
except:
if self.verify_species_exists:
raise CommandError("Species {} not found".format(wid))
else:
species_obj = Species(wid = wid)
if not options["user"]:
options["user"] = "******"
revdetail = RevisionDetail()
revdetail.user = UserProfile.objects.get(user__username = options["user"])
revdetail.reason = reason
revdetail.save()
self.handle_command(species_obj, revdetail, *args, **options)
def try_slugify(self, name, not_slug):
slug = slugify(not_slug)
if slug != not_slug:
raise ValueError("{} {} contained invalid characters. Only letters, numbers and _ are allowed".format(name, not_slug))
return slug
def _import_protein_summary(self, ms_job):
# Import the protein data from the file
for row in self.protein_summary:
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Protein Summary ({})".format(
row["ID"])
self.current += 1
self.notify_progress(current=self.current,
total=self.total,
message=outstr)
protein = cmodels.MassSpectrometryProtein.objects.for_species(
self.species).for_wid(slugify(row["ID"]), create=True)
""":type: cmodels.MassSpectrometryProtein"""
protein.comments = row["Description"]
uniprot = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="UniProt", xid=row["AC"])
protein.score = row["Protein Score"]
protein.coverage = row["% Coverage"]
protein.sequence = row["Protein Seq"]
protein.length = len(protein.sequence)
# #PSMs -> Peptide spectrum match -> Entries in Details
# #Peptides -> Count number of different sequences(?) in Details
protein.pi = row["Protein PI"]
protein.mass = row["Protein Mass (Da)"]
protein.parent = ms_job
protein.species = self.species
protein.save(self.detail)
protein.cross_references.add(uniprot)
# Extract all GO terms splitted to a generator containing list
# [name, type (GO), identifier]
go_term_row = row["GO terms"]
if go_term_row:
go_terms = (x.groups()
for x in (re.match(r"^(.*) \((.*):(.*)\)$", x)
for x in go_term_row.split(";") if x))
for name, typ, identifier in go_terms:
go = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=typ, xid=identifier)
protein.cross_references.add(go)
# No field for name :/
if row["#Ambiguous Prots"] > 0:
for amb_protein in row["Ambiguous Prots"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(
self.detail, value=amb_protein.strip())
protein.ambiguous.add(prot)
if row["#Sub-Prots"] > 0:
for sub_protein in row["Sub-Prots"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(
self.detail, value=sub_protein.strip())
protein.sub.add(prot)
def parse(self, handle):
if hasattr(self, "notify_progress"):
self.notify_progress(current=0, total=1, message="Parsing InterProScan file...")
xml = handle.read()
# Remove xmlns namespace, makes working with ElementTree more complicated
xml = re.sub(' xmlns="[^"]+"', '', xml, count=1)
root = ET.fromstring(xml)
all_proteins = root.findall("protein")
all_proteins_len = len(all_proteins)
for i, protein in enumerate(all_proteins):
xref = protein.find("xref")
wid = xref.get("id").split("|", 2)[0]
self.total = all_proteins_len
if hasattr(self, "notify_progress"):
self.notify_progress(current=i+1, total=self.total, message="Parsing features of {} ({}/{})".
format(wid, i+1, self.total))
try:
protein_item = cmodels.ProteinMonomer.objects.for_species(self.species).for_wid(wid)
self.protein_monomers_cf[protein_item] = []
except ObjectDoesNotExist:
# ToDo: Error reporting?
continue
for matches in protein.findall("matches"):
for match in matches:
signature = match.find("signature")
wid = slugify(signature.get("ac"))
cf = cmodels.ChromosomeFeature(wid=wid)
cf.name = signature.get("name") or ""
cf.comments = signature.get("desc") or ""
self.xrefs[wid] = []
self.protein_monomers_cf[protein_item].append(cf)
self.types[wid] = match.tag.title()
for entry in signature.findall("entry"):
for xref in entry:
self.xrefs[wid].append([xref.get("id"), xref.get("db")])
self.feature_positions[wid] = []
locations = match.find("locations")
for location in locations:
start = int(location.get("start"))
end = int(location.get("end"))
direction = "f"
if start > end:
start, end = end, start
direction = "r"
length = end - start
self.feature_positions[wid].append({"chromosome": protein_item.gene.chromosome_id,
"coordinate": start + protein_item.gene.coordinate,
"length": length,
"direction": direction})
def _import_jobs_params(self):
ms_job = cmodels.MassSpectrometryJob.objects.for_species(
self.species).for_wid(slugify(
self.export_parameters["jobs"][0][0]),
create=True)
ms_job.name = ms_job.wid
ms_job.species = self.species
ms_job.save(self.detail)
return ms_job
def parse(self, handle):
self.report_progress(current=0, total=1, message="Parsing FASTA file")
for record in SeqIO.parse(handle, "fasta"):
wid, start, end, description = FastaFeature._parse_header(record.description)
wid = slugify(wid)
self.data.append({
"wid": wid,
"start": int(start),
"end": int(end),
"description": description
})
def parse(self, handle):
self.report_progress(current=0, total=1, message="Parsing FASTA file")
for record in SeqIO.parse(handle, "fasta"):
wid, start, end, description = FastaFeature._parse_header(
record.description)
wid = slugify(wid)
self.data.append({
"wid": wid,
"start": int(start),
"end": int(end),
"description": description
})
def _import_protein_summary(self, ms_job):
# Import the protein data from the file
for row in self.protein_summary:
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Protein Summary ({})".format(row["ID"])
self.current += 1
self.notify_progress(current=self.current, total=self.total, message=outstr)
protein = cmodels.MassSpectrometryProtein.objects.for_species(self.species).for_wid(slugify(row["ID"]), create=True)
""":type: cmodels.MassSpectrometryProtein"""
protein.comments = row["Description"]
uniprot = cmodels.CrossReference.objects.get_or_create_with_revision(self.detail, source="UniProt", xid=row["AC"])
protein.score = row["Protein Score"]
protein.coverage = row["% Coverage"]
protein.sequence = row["Protein Seq"]
protein.length = len(protein.sequence)
# #PSMs -> Peptide spectrum match -> Entries in Details
# #Peptides -> Count number of different sequences(?) in Details
protein.pi = row["Protein PI"]
protein.mass = row["Protein Mass (Da)"]
protein.parent = ms_job
protein.species = self.species
protein.save(self.detail)
protein.cross_references.add(uniprot)
# Extract all GO terms splitted to a generator containing list
# [name, type (GO), identifier]
go_term_row = row["GO terms"]
if go_term_row:
go_terms = (x.groups() for x in (re.match(r"^(.*) \((.*):(.*)\)$", x) for x in go_term_row.split(";") if x))
for name, typ, identifier in go_terms:
go = cmodels.CrossReference.objects.get_or_create_with_revision(self.detail, source=typ, xid=identifier)
protein.cross_references.add(go)
# No field for name :/
if row["#Ambiguous Prots"] > 0:
for amb_protein in row["Ambiguous Prots"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(self.detail, value=amb_protein.strip())
protein.ambiguous.add(prot)
if row["#Sub-Prots"] > 0:
for sub_protein in row["Sub-Prots"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(self.detail, value=sub_protein.strip())
protein.sub.add(prot)
def _import_target_peptides(self, ms_job):
target_type = cmodels.Type.objects.for_wid("Target-Peptide", create=True)
target_type.species = self.species
target_type.save(self.detail)
for i, item in enumerate(self.target_peptides):
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Target Peptide ({})".format(item["Matched Proteins"])
self.current += 1
self.notify_progress(current=self.current, total=self.total, message=outstr)
peptide = cmodels.Peptide.objects.for_species(self.species).for_wid("{}-{}".format(i+1, slugify(item["Matched Proteins"])), create=True)
peptide.parent = ms_job
peptide.sequence = item["Sequence"]
peptide.length = len(item["Sequence"])
peptide.proteotypic = item["Proteotypic"]
peptide.charge = item["Charge"]
peptide.mass = item["m/z"]
peptide.zscore = item["zscore"]
peptide.retention_time = item["RT"]
peptide.species = self.species
peptide.save(self.detail)
peptide.type.add(target_type)
for protein in item["Matched Proteins"].split(","):
prot = cmodels.EntryBasicTextData.objects.get_or_create_with_revision(self.detail, value=protein.strip())
peptide.proteins.add(prot)
def _import_jobs_params(self):
ms_job = cmodels.MassSpectrometryJob.objects.for_species(self.species).for_wid(slugify(self.export_parameters["jobs"][0][0]), create=True)
ms_job.name = ms_job.wid
ms_job.species = self.species
ms_job.save(self.detail)
return ms_job
def parse(self, handle):
if hasattr(self, "notify_progress"):
self.notify_progress(current=0,
total=1,
message="Parsing InterProScan file...")
xml = handle.read()
# Remove xmlns namespace, makes working with ElementTree more complicated
xml = re.sub(' xmlns="[^"]+"', '', xml, count=1)
root = ET.fromstring(xml)
all_proteins = root.findall("protein")
all_proteins_len = len(all_proteins)
for i, protein in enumerate(all_proteins):
xref = protein.find("xref")
wid = xref.get("id").split("|", 2)[0]
self.total = all_proteins_len
if hasattr(self, "notify_progress"):
self.notify_progress(
current=i + 1,
total=self.total,
message="Parsing features of {} ({}/{})".format(
wid, i + 1, self.total))
try:
protein_item = cmodels.ProteinMonomer.objects.for_species(
self.species).for_wid(wid)
self.protein_monomers_cf[protein_item] = []
except ObjectDoesNotExist:
# ToDo: Error reporting?
continue
for matches in protein.findall("matches"):
for match in matches:
signature = match.find("signature")
wid = slugify(signature.get("ac"))
cf = cmodels.ChromosomeFeature(wid=wid)
cf.name = signature.get("name") or ""
cf.comments = signature.get("desc") or ""
self.xrefs[wid] = []
self.protein_monomers_cf[protein_item].append(cf)
self.types[wid] = match.tag.title()
for entry in signature.findall("entry"):
for xref in entry:
self.xrefs[wid].append(
[xref.get("id"),
xref.get("db")])
self.feature_positions[wid] = []
locations = match.find("locations")
for location in locations:
start = int(location.get("start"))
end = int(location.get("end"))
direction = "f"
if start > end:
start, end = end, start
direction = "r"
length = end - start
self.feature_positions[wid].append({
"chromosome":
protein_item.gene.chromosome_id,
"coordinate":
start + protein_item.gene.coordinate,
"length":
length,
"direction":
direction
})
def apply(self):
self.detail.save()
self.species.save(self.detail)
obj = cmodels.Chromosome if self.is_chromosome else cmodels.Plasmid
chromosome = obj.objects.for_species(self.species).for_wid(
self.chromosome, create=True)
chromosome.name = self.name
chromosome.sequence = str(
self.record.seq) # Cast needed, otherwise revision-compare fails!
chromosome.length = len(self.record.seq)
chromosome.species = self.species
chromosome.save(self.detail)
if self.record.dbxrefs:
for xref in self.record.dbxrefs:
# BioPython doesnt always properly split the db xrefs
xref = xref.split(" ")
for x in xref:
if ":" in x:
source, xid = x.split(":")
x = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid)
chromosome.cross_references.add(x)
if "references" in self.annotation:
for ref in self.annotation["references"]:
# calculate the wid
if ref.pubmed_id:
wid = "PUB_" + ref.pubmed_id
name = "Pubmed #" + ref.pubmed_id
elif ref.medline_id:
wid = "MED_" + ref.medline_id
name = "Pubmed #" + ref.medline_id
else:
publication = cmodels.PublicationReference.objects.filter(
authors__exact=ref.authors,
title__exact=ref.title,
publication__exact=ref.journal)
next_id = 0
if publication.exists():
wid = publication[0].wid
name = publication[0].name
else:
refs = cmodels.PublicationReference.objects.filter(
wid__startswith="REF_")
if refs.exists():
last = refs.reverse()[0]
next_id = int(last.wid[4:], 10) + 1
wid = "REF_" + "%04d" % (next_id)
name = "Reference #%04d" % (next_id)
else:
wid = "REF_0001"
name = "Reference #0001"
pubref = cmodels.PublicationReference.objects.for_wid(
slugify(wid), create=True)
pubref.name = name
pubref.authors = ref.authors
pubref.title = ref.title
pubref.publication = ref.journal
pubref.species = self.species
pubref.save(self.detail)
if ref.pubmed_id:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="PUBMED", xid=ref.pubmed_id)
pubref.cross_references.add(xref)
if ref.medline_id:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="MEDLINE", xid=ref.medline_id)
pubref.cross_references.add(xref)
chromosome.publication_references.add(pubref)
if "gi" in self.annotation:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, xid=self.annotation["gi"], source="GI")
chromosome.cross_references.add(xref)
features = self.record.features
if len(features) > 0:
if features[0].type == "source":
if "db_xref" in features[0].qualifiers:
for xref in features[0].qualifiers["db_xref"]:
if ":" in xref:
source, xid = xref.split(":")
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid)
chromosome.cross_references.add(xref)
gene_features = filter(lambda x: x.type == "gene", features)
cds_features = filter(
lambda x: x.type in ["CDS", "ncRNA", "rRNA", "tmRNA", "tRNA"],
features)
gene_map = {}
for g in gene_features:
if not "locus_tag" in g.qualifiers:
self.stderr.write("WARN: " + str(g) + " without locus")
continue
loci = g.qualifiers["locus_tag"][0]
if loci in gene_map:
raise ValueError("locus_tag " + loci + " appeared twice")
gene_map[loci] = g
cds_map = {}
for c in cds_features:
if not "locus_tag" in c.qualifiers:
self.stderr.write("WARN: " + str(c) + " without locus")
continue
loci = c.qualifiers["locus_tag"][0]
if loci in cds_map:
raise ValueError("locus_tag " + loci + " appeared twice")
if loci in gene_map:
cds_map[loci] = c
sorted_cds_values = sorted(cds_map.values(),
key=lambda x: x.qualifiers["locus_tag"])
for i, v in enumerate(sorted_cds_values):
qualifiers = v.qualifiers
if not self.species.genetic_code:
if "transl_table" in qualifiers:
self.species.genetic_code = qualifiers["transl_table"][0]
self.species.save(self.detail)
g = cmodels.Gene.objects.for_species(self.species).for_wid(
slugify(qualifiers["locus_tag"][0]), create=True)
if hasattr(self, "notify_progress"):
outstr = "Importing Gene %s (%d/%d)" % (g.wid, i + 1,
len(cds_map.values()))
self.notify_progress(current=i + 1,
total=len(cds_map.values()),
message=outstr)
g.chromosome = chromosome
if "gene" in qualifiers:
g.name = qualifiers["gene"][0]
g.symbol = qualifiers["gene"][0]
g.direction = 'f' if v.location.strand == 1 else 'r'
# __len__ because len() fails for numbers < 0
# Joins output the wrong length
if v.location.__len__() < 0:
g.length = v.location.__len__() + len(self.record.seq)
else:
g.length = len(v.location)
g.coordinate = v.location.start + 1 if 'f' else v.location.start
if "note" in qualifiers:
g.comments = "\n".join(qualifiers["note"])
g.species = self.species
g.save(self.detail)
if "db_xref" in qualifiers:
for xref in qualifiers["db_xref"]:
if ":" in xref:
source, xid = xref.split(":")
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid)
g.cross_references.add(xref)
if "EC_number" in qualifiers:
for ec in qualifiers["EC_number"]:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="EC", xid=ec)
g.cross_references.add(xref)
if "gene_synonym" in qualifiers:
for synonym in qualifiers["gene_synonym"]:
# Inconsistency: Multiple synonyms appear in one entry,
# why don't they split them like for all other items?
for syn in synonym.split(";"):
obj = cmodels.Synonym.objects.get_or_create_with_revision(
self.detail, name=syn.strip())
g.synonyms.add(obj)
if "protein_id" in qualifiers:
protxref = qualifiers["protein_id"][0]
wid = slugify(g.wid + "_Monomer")
protein = cmodels.ProteinMonomer.objects.for_species(
self.species).for_wid(wid, create=True)
if "product" in qualifiers:
protein.name = qualifiers["product"][0]
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="RefSeq", xid=protxref)
protein.gene = g
protein.species = self.species
protein.save(self.detail)
protein.cross_references.add(xref)
if v.type == "CDS":
v.type = "mRNA"
t = cmodels.Type.objects.for_wid(wid=slugify(v.type), create=True)
t.name = v.type
t.species = self.species
t.save(self.detail)
g.type.add(t)
if hasattr(self, "notify_progress"):
outstr = "Assigning KEGG pathways"
self.notify_progress(current=len(cds_map.values()),
total=len(cds_map.values()),
message=outstr)
cmodels.Pathway.add_kegg_pathway(self.species, self.detail)
def apply(self):
self.detail.save()
total = len(self.compartments) + len(self.sbml_species) + len(self.reactions)
# Compartment importer
for i, compartment in enumerate(self.compartments):
wid = slugify(compartment.getId())
if compartment.getName():
name = compartment.getName()
else:
name = wid
if hasattr(self, "notify_progress"):
out_str = "Importing Compartment %s (%d/%d)" % (wid, i + 1, total)
self.notify_progress(current = i+1, total = total, message = out_str)
# TODO: compartment.getOutside() not implemented
cobj = cmodels.Compartment.objects.for_species(self.species).for_wid(wid, create = True)
cobj.name = name
cobj.species = self.species
cobj.save(self.detail)
# Species (= Metabolites) importer
for i, specie in enumerate(self.sbml_species):
if not self.model.getCompartment(specie.getCompartment()):
##self.stderr.write("WARN: Species {} has invalid compartment {}".format(specie.id, specie.getCompartment()))
continue
wid = slugify(specie.getId())
if specie.getName():
name = specie.getName()
else:
name = wid
if hasattr(self, "notify_progress"):
current = len(self.compartments) + i + 1
out_str = "Importing Metabolite %s (%d/%d)" % (wid, current, total)
self.notify_progress(current = current, total = total, message = out_str)
# TODO: specie.getBoundaryCondition() not implemented
sobj = cmodels.Metabolite.objects.for_species(self.species).for_wid(wid, create = True)
sobj.name = name
sobj.charge = 0 # TODO
sobj.is_hydrophobic = False # TODO
sobj.species = self.species
sobj.save(self.detail)
for i, reaction in enumerate(self.reactions):
wid = slugify(reaction.getId())
if reaction.getName():
name = reaction.getName()
else:
name = wid
valid = False
if hasattr(self, "notify_progress"):
current = len(self.compartments) + len(self.sbml_species) + i + 1
out_str = "Importing Reaction %s (%d/%d)" % (wid, current, total)
self.notify_progress(current = current, total = total, message = out_str)
# Validation of reactants
reactants = map(lambda i: reaction.getReactant(i), range(len(reaction.getListOfReactants())))
products = map(lambda i: reaction.getProduct(i), range(len(reaction.getListOfProducts())))
for reactant in reactants:
if not self.model.getSpecies(reactant.getSpecies()):
##self.stderr.write("WARN: Reactant {} has invalid species {}".format(reactant.id, reactant.species))
break
else:
# Validation of products
for product in products:
if not self.model.getSpecies(product.getSpecies()):
##self.stderr.write("WARN: Product {} has invalid species {}".format(product.id, product.species))
break
else:
# Validation passed
valid = True
if valid:
reaction_obj = cmodels.Reaction.objects.for_species(self.species).for_wid(wid, create = True)
reaction_obj.name = name
reaction_obj.direction = 'r' if reaction.getReversible() else 'f'
reaction_obj.is_spontaneous = False # TODO
reaction_obj.species = self.species
reaction_obj.save(self.detail)
for reactant in reactants:
#try:
# participant_obj = cmodels.ReactionStoichiometryParticipant.objects.get(wid = wid)
#except ObjectDoesNotExist:
# participant_obj = cmodels.ReactionStoichiometryParticipant(wid = wid)
participant_obj = cmodels.ReactionStoichiometryParticipant()
participant_obj.molecule = cmodels.Metabolite.objects.for_species(self.species).for_wid(slugify(reactant.getSpecies()))
participant_obj.coefficient = -reactant.getStoichiometry()
participant_obj.compartment = cmodels.Compartment.objects.for_species(self.species).for_wid(slugify(self.model.getSpecies(reactant.getSpecies()).getCompartment()))
participant_obj.save(self.detail)
reaction_obj.stoichiometry.add(participant_obj)
for product in products:
#try:
# participant_obj = cmodels.ReactionStoichiometryParticipant.objects.get(wid = wid)
#except ObjectDoesNotExist:
# participant_obj = cmodels.ReactionStoichiometryParticipant(wid = wid)
participant_obj = cmodels.ReactionStoichiometryParticipant()
participant_obj.molecule = cmodels.Metabolite.objects.for_species(self.species).for_wid(slugify(product.getSpecies()))
participant_obj.coefficient = product.getStoichiometry()
participant_obj.compartment = cmodels.Compartment.objects.for_species(self.species).for_wid(slugify(self.model.getSpecies(product.getSpecies()).getCompartment()))
participant_obj.detail = self.detail
participant_obj.save(self.detail)
reaction_obj.stoichiometry.add(participant_obj)
def _import_protein_details(self, ms_job):
for row in self.protein_details:
if hasattr(self, "notify_progress"):
outstr = "EasyProt: Importing Protein Details ({})".format(row["ID"])
self.current += 1
self.notify_progress(current=self.current, total=self.total, message=outstr)
ref_protein = cmodels.MassSpectrometryProtein.objects.for_species(self.species).for_wid(slugify(row["ID"]))
coordinate, length = map(lambda x: int(x), row["Position (to mature prot.)"].split("-"))
cmodels.MassSpectrometryProteinDetail.objects.get_or_create_with_revision(
self.detail,
protein=ref_protein,
sequence=row["Sequence"],
sequence_ptm=row["Sequence + PTMs"],
coordinate=coordinate,
length=length-coordinate,
proteotypic=row["Proteotypic"],
zscore=row["z-score"],
delta_mass=row["Delta Mass (ppm)"],
mass=row["Experimental Mass (m/z)"],
charge=row["Charge"],
retention_time=row["Retention Time (min)"],
theoretical_mass=row["Theoretical Mass (Da)"],
missed_cleavages=row["Missed Cleavages"]
)
def apply(self):
self.detail.save()
self.species.save(self.detail)
obj = cmodels.Chromosome if self.is_chromosome else cmodels.Plasmid
chromosome = obj.objects.for_species(self.species).for_wid(self.chromosome, create=True)
chromosome.name = self.name
chromosome.sequence = str(self.record.seq) # Cast needed, otherwise revision-compare fails!
chromosome.length = len(self.record.seq)
chromosome.species = self.species
chromosome.save(self.detail)
if self.record.dbxrefs:
for xref in self.record.dbxrefs:
# BioPython doesnt always properly split the db xrefs
xref = xref.split(" ")
for x in xref:
if ":" in x:
source, xid = x.split(":")
x = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid
)
chromosome.cross_references.add(x)
if "references" in self.annotation:
for ref in self.annotation["references"]:
# calculate the wid
if ref.pubmed_id:
wid = "PUB_" + ref.pubmed_id
name = "Pubmed #" + ref.pubmed_id
elif ref.medline_id:
wid = "MED_" + ref.medline_id
name = "Pubmed #" + ref.medline_id
else:
publication = cmodels.PublicationReference.objects.filter(
authors__exact=ref.authors, title__exact=ref.title, publication__exact=ref.journal
)
next_id = 0
if publication.exists():
wid = publication[0].wid
name = publication[0].name
else:
refs = cmodels.PublicationReference.objects.filter(wid__startswith="REF_")
if refs.exists():
last = refs.reverse()[0]
next_id = int(last.wid[4:], 10) + 1
wid = "REF_" + "%04d" % (next_id)
name = "Reference #%04d" % (next_id)
else:
wid = "REF_0001"
name = "Reference #0001"
pubref = cmodels.PublicationReference.objects.for_wid(slugify(wid), create=True)
pubref.name = name
pubref.authors = ref.authors
pubref.title = ref.title
pubref.publication = ref.journal
pubref.species = self.species
pubref.save(self.detail)
if ref.pubmed_id:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="PUBMED", xid=ref.pubmed_id
)
pubref.cross_references.add(xref)
if ref.medline_id:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="MEDLINE", xid=ref.medline_id
)
pubref.cross_references.add(xref)
chromosome.publication_references.add(pubref)
if "gi" in self.annotation:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, xid=self.annotation["gi"], source="GI"
)
chromosome.cross_references.add(xref)
features = self.record.features
if len(features) > 0:
if features[0].type == "source":
if "db_xref" in features[0].qualifiers:
for xref in features[0].qualifiers["db_xref"]:
if ":" in xref:
source, xid = xref.split(":")
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid
)
chromosome.cross_references.add(xref)
gene_features = filter(lambda x: x.type == "gene", features)
cds_features = filter(lambda x: x.type in ["CDS", "ncRNA", "rRNA", "tmRNA", "tRNA"], features)
gene_map = {}
for g in gene_features:
if not "locus_tag" in g.qualifiers:
self.stderr.write("WARN: " + str(g) + " without locus")
continue
loci = g.qualifiers["locus_tag"][0]
if loci in gene_map:
raise ValueError("locus_tag " + loci + " appeared twice")
gene_map[loci] = g
cds_map = {}
for c in cds_features:
if not "locus_tag" in c.qualifiers:
self.stderr.write("WARN: " + str(c) + " without locus")
continue
loci = c.qualifiers["locus_tag"][0]
if loci in cds_map:
raise ValueError("locus_tag " + loci + " appeared twice")
if loci in gene_map:
cds_map[loci] = c
sorted_cds_values = sorted(cds_map.values(), key=lambda x: x.qualifiers["locus_tag"])
for i, v in enumerate(sorted_cds_values):
qualifiers = v.qualifiers
if not self.species.genetic_code:
if "transl_table" in qualifiers:
self.species.genetic_code = qualifiers["transl_table"][0]
self.species.save(self.detail)
g = cmodels.Gene.objects.for_species(self.species).for_wid(slugify(qualifiers["locus_tag"][0]), create=True)
if hasattr(self, "notify_progress"):
outstr = "Importing Gene %s (%d/%d)" % (g.wid, i + 1, len(cds_map.values()))
self.notify_progress(current=i + 1, total=len(cds_map.values()), message=outstr)
g.chromosome = chromosome
if "gene" in qualifiers:
g.name = qualifiers["gene"][0]
g.symbol = qualifiers["gene"][0]
g.direction = "f" if v.location.strand == 1 else "r"
# __len__ because len() fails for numbers < 0
# Joins output the wrong length
if v.location.__len__() < 0:
g.length = v.location.__len__() + len(self.record.seq)
else:
g.length = len(v.location)
g.coordinate = v.location.start + 1 if "f" else v.location.start
if "note" in qualifiers:
g.comments = "\n".join(qualifiers["note"])
g.species = self.species
g.save(self.detail)
if "db_xref" in qualifiers:
for xref in qualifiers["db_xref"]:
if ":" in xref:
source, xid = xref.split(":")
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source=source, xid=xid
)
g.cross_references.add(xref)
if "EC_number" in qualifiers:
for ec in qualifiers["EC_number"]:
xref = cmodels.CrossReference.objects.get_or_create_with_revision(self.detail, source="EC", xid=ec)
g.cross_references.add(xref)
if "gene_synonym" in qualifiers:
for synonym in qualifiers["gene_synonym"]:
# Inconsistency: Multiple synonyms appear in one entry,
# why don't they split them like for all other items?
for syn in synonym.split(";"):
obj = cmodels.Synonym.objects.get_or_create_with_revision(self.detail, name=syn.strip())
g.synonyms.add(obj)
if "protein_id" in qualifiers:
protxref = qualifiers["protein_id"][0]
wid = slugify(g.wid + "_Monomer")
protein = cmodels.ProteinMonomer.objects.for_species(self.species).for_wid(wid, create=True)
if "product" in qualifiers:
protein.name = qualifiers["product"][0]
xref = cmodels.CrossReference.objects.get_or_create_with_revision(
self.detail, source="RefSeq", xid=protxref
)
protein.gene = g
protein.species = self.species
protein.save(self.detail)
protein.cross_references.add(xref)
if v.type == "CDS":
v.type = "mRNA"
t = cmodels.Type.objects.for_wid(wid=slugify(v.type), create=True)
t.name = v.type
t.species = self.species
t.save(self.detail)
g.type.add(t)
if hasattr(self, "notify_progress"):
outstr = "Assigning KEGG pathways"
self.notify_progress(current=len(cds_map.values()), total=len(cds_map.values()), message=outstr)
cmodels.Pathway.add_kegg_pathway(self.species, self.detail)