def ma_run(partition):
log = task.logger
config = GlobalConfig(task.conf)
results_port = task.ports("results")
project = partition["project"]
log.info("--- [{0} @ {1}] --------------------------------------------".format(project["id"], partition["index"]))
offline = "yes" # TODO: deprecate online mode
if offline == "yes":
log.info("Running Mutation assessor in local mode.")
ma = MaLocal(config.ma_cache_path)
else:
log.info("Running Mutation assessor using web services.")
from intogensm.ma.service import MaService
ma = MaService(project["assembly"], cache_path=os.path.join(conf["cache_path"], "ma.db"))
results_path = os.path.join(partition["base_path"], "{0:08d}.ma".format(partition["index"]))
if not os.path.exists(results_path) or config.consequences_overwrite:
log.info("Querying Mutation assessor for 'missense_variant' consequences ...")
projdb = ProjectDb(project["db"])
missense_variants = set()
with open(partition["vep_path"], "r") as f:
for line in f:
fields = line.rstrip().split("\t")
var_id = int(fields[0])
ctypes = fields[3].split(",")
if so.match(ctypes, so.NON_SYNONYMOUS):
missense_variants.add(var_id)
with open(results_path, "w") as mf:
for var_id in missense_variants:
var = projdb.get_variant(var_id)
start, end, ref, alt = var_to_tab(var)
r = ma.get(var.chr, var.strand, start, ref, alt, var_id)
if r is not None:
tsv.write_line(mf, var_id, r.uniprot, r.fi_score, null_value="-")
projdb.close()
else:
log.warn("Skipping MA, results already exist.")
log.debug("MA results: {0}".format(results_path))
ma.close()
# Send results to the next module
partition["ma_path"] = results_path
results_port.send(partition)
def update_db(project):
log = task.logger
config = GlobalConfig(task.conf)
projects_port = task.ports("projects_out")
log.info("--- [{0}] --------------------------------------------".format(project["id"]))
partitions = project["partitions"]
if not os.path.exists(config.vardb_path):
log.warn("Database for variation external references not found")
log.debug("> {0}".format(conf["vardb_path"]))
varxdb = VarXrefsDb(config.vardb_path)
varxdb.open()
projdb = ProjectDb(project["db"])
updated_variants = set()
plen = len(partitions)
gene_xrefs = defaultdict(set)
for part in partitions:
log.info("Updating database with partition data ({0} out of {1}) ...".format(part["index"] + 1, plen))
log.info(" VEP results ...")
ctype = lambda v: v.split(",")
with open(part["vep_path"], "r") as vf:
for fields in tsv.lines(vf, (int, str, str, ctype, str, str, str, float, float), null_value="-"):
(
var_id,
gene,
transcript,
consequences,
protein_pos,
aa_change,
protein,
sift_score,
pph2_score,
) = fields
var = projdb.get_variant(var_id)
xrefs = varxdb.get_xrefs(var.chr, var.start, var.ref, var.alt, var.strand)
if xrefs is not None:
xrefs = ["{0}:{1}".format(source, xref) for source, xref in xrefs]
gene_xrefs[gene].update(xrefs)
if len(xrefs) == 0:
xrefs = None
projdb.update_variant(Variant(id=var_id, xrefs=xrefs))
projdb.add_consequence(
Consequence(
var=Variant(id=var_id),
transcript=transcript,
gene=gene,
ctypes=consequences,
protein_pos=protein_pos,
aa_change=aa_change,
protein=protein,
)
)
log.info(" Transcript functional impacts ...")
with open(part["tfi_path"], "r") as f:
types = (int, str, str, int, float, float, int, float, float, int, float, float, int)
columns = [0, 1, 3, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17]
for fields in tsv.lines(f, types, columns=columns, null_value="-"):
(
var_id,
transcript,
uniprot,
impact,
sift_score,
sift_tfic,
sift_class,
pph2_score,
pph2_tfic,
pph2_class,
ma_score,
ma_tfic,
ma_class,
) = fields
print fields
projdb.update_consequence(
Consequence(
var=Variant(id=var_id),
transcript=transcript,
uniprot=uniprot,
sift_score=sift_score,
sift_tfic=sift_tfic,
sift_tfic_class=sift_class,
pph2_score=pph2_score,
pph2_tfic=pph2_tfic,
pph2_tfic_class=pph2_class,
ma_score=ma_score,
ma_tfic=ma_tfic,
ma_tfic_class=ma_class,
impact=impact,
)
)
log.info("Updating variant-gene functional impacts ...")
with open(project["gfi_path"], "r") as f:
types = (int, str, float, int, str)
for var_id, gene, impact, coding_region, prot_changes in tsv.lines(f, types, null_value="-"):
projdb.add_affected_gene(
AffectedGene(
var=Variant(id=var_id),
gene_id=gene,
impact=impact,
coding_region=coding_region,
prot_changes=prot_changes,
)
)
log.info("Updating database with gene external variant references ...")
for gene, xrefs in gene_xrefs.items():
projdb.update_gene(Gene(id=gene, xrefs=xrefs))
projdb.commit()
projdb.close()
varxdb.close()
del project["partitions"]
projects_port.send(project)
