def split_variants(project):
log = task.logger
config = GlobalConfig(task.conf)
partition_port = task.ports("partitions")
log.info("--- [{}] --------------------------------------------".format(project["id"]))
projdb = ProjectDb(project["db"])
log.info("Preparing variants for VEP ...")
base_path = os.path.join(project["temp_path"], "consequences")
ensure_path_exists(base_path)
project["csq_path"] = base_path
partition_size = config.vep_partition_size
partition = -1
f = None
count = 0
for var in projdb.variants(order_by="position"):
start, end, ref, alt = var_to_tab(var)
if count % partition_size == 0:
if f is not None:
f.close()
partition += 1
partition_path = os.path.join(base_path, "{0:08d}.vep_in".format(partition))
f = open(partition_path, "w")
partition_port.send(
{"project": project, "index": partition, "bed_path": partition_path, "base_path": base_path}
)
tsv.write_line(f, var.chr, start, end, ref + "/" + alt, var.strand, var.id)
count += 1
if f is not None:
f.close()
log.info("{} variants split into {} partitions".format(count, partition + 1))
projdb.close()
def pack_datasets(project):
log = task.logger
config = GlobalConfig(task.conf)
project_id = project["id"]
log.info("--- [{0}] --------------------------------------------".format(project_id))
if not config.results.create_zip:
log.info("Creation of the results compressed file is deactivated. Skipped.")
return
project_path = project["path"]
temp_path = project["temp_path"]
dest_path = os.path.join(project_path, "results.zip")
sigdb = SigDb(config.sigdb_path)
sigdb.open()
projdb = ProjectDb(project["db"])
projres = ProjectResults(project)
gene_sym = projdb.get_gene_symbols()
total_samples = projdb.get_total_affected_samples()
log.info("Compressing files ...")
arc = None
try:
arc = Archive(dest_path, mode="w", fmt="zip")
log.info(" Variant genes ...")
with ArcFile(task, arc, project_id, "variant_genes", "w") as vf:
write_line(vf, "PROJECT_ID", "CHR", "STRAND", "START", "ALLELE",
"GENE_ID", "SYMBOL", "VAR_IMPACT", "VAR_IMPACT_DESC",
"SAMPLE_FREQ", "SAMPLE_TOTAL", "SAMPLE_PROP",
"CODING_REGION", "PROTEIN_CHANGES", "INTOGEN_DRIVER", "XREFS")
for afg in projdb.affected_genes(join_variant=True, join_xrefs=True, join_rec=True):
var = afg.var
rec = afg.rec
start, end, ref, alt = var_to_tab(var)
xrefs = [xref for xref in var.xrefs]
if sigdb.exists_variant(var.chr, start):
xrefs += ["I:1"]
xrefs = ",".join(xrefs)
intogen_driver = 1 if sigdb.exists_gene(afg.gene_id) else 0
write_line(vf, project_id, var.chr, var.strand, start, "{0}/{1}".format(ref, alt),
afg.gene_id, gene_sym.get(afg.gene_id),
afg.impact, TransFIC.class_name(afg.impact),
rec.sample_freq or 0, total_samples, rec.sample_prop or 0,
afg.coding_region, afg.prot_changes, intogen_driver, xrefs)
log.info(" Variant samples ...")
with ArcFile(task, arc, project_id, "variant_samples", "w") as vf:
write_line(vf, "PROJECT_ID", "CHR", "STRAND", "START", "ALLELE", "SAMPLES")
for var in projdb.variants(join_samples=True):
start, end, ref, alt = var_to_tab(var)
write_line(vf, project_id, var.chr, var.strand, start, "{0}/{1}".format(ref, alt),
",".join([s.name for s in var.samples]))
log.info(" Consequences ...")
with ArcFile(task, arc, project_id, "consequences", "w") as cf:
write_line(cf, "PROJECT_ID", "CHR", "STRAND", "START", "ALLELE", "TRANSCRIPT_ID", "CT",
"GENE_ID", "SYMBOL", "UNIPROT_ID", "PROTEIN_ID", "PROTEIN_POS", "AA_CHANGE",
"SIFT_SCORE", "SIFT_TRANSFIC", "SIFT_TRANSFIC_CLASS",
"PPH2_SCORE", "PPH2_TRANSFIC", "PPH2_TRANSFIC_CLASS",
"MA_SCORE", "MA_TRANSFIC", "MA_TRANSFIC_CLASS",
"IMPACT", "IMPACT_CLASS")
for csq in projdb.consequences(join_variant=True):
var = csq.var
start, end, ref, alt = var_to_tab(var)
allele = "{0}/{1}".format(ref, alt)
uniprot = protein = protein_pos = aa_change = None
sift_score = sift_tfic = sift_tfic_class = None
pph2_score = pph2_tfic = pph2_tfic_class = None
ma_score = ma_tfic = ma_tfic_class = None
if so.match(csq.ctypes, so.ONCODRIVEFM):
uniprot, protein = csq.uniprot, csq.protein
if so.match(csq.ctypes, so.NON_SYNONYMOUS):
protein_pos, aa_change = csq.protein_pos, csq.aa_change
sift_score, sift_tfic, sift_tfic_class = csq.sift_score, csq.sift_tfic, TransFIC.class_name(csq.sift_tfic_class)
pph2_score, pph2_tfic, pph2_tfic_class = csq.pph2_score, csq.pph2_tfic, TransFIC.class_name(csq.pph2_tfic_class)
ma_score, ma_tfic, ma_tfic_class = csq.ma_score, csq.ma_tfic, TransFIC.class_name(csq.ma_tfic_class)
write_line(cf, project_id, var.chr, var.strand, start, allele, csq.transcript,
",".join(csq.ctypes), csq.gene, gene_sym.get(csq.gene),
uniprot, protein, protein_pos, aa_change,
sift_score, sift_tfic, sift_tfic_class,
pph2_score, pph2_tfic, pph2_tfic_class,
ma_score, ma_tfic, ma_tfic_class,
csq.impact, TransFIC.class_name(csq.impact))
log.info(" Genes ...")
with ArcFile(task, arc, project_id, "genes", "w") as gf:
write_line(gf, "PROJECT_ID", "GENE_ID", "SYMBOL", "FM_PVALUE", "FM_QVALUE", "FM_EXC_CAUSE",
"SAMPLE_FREQ", "SAMPLE_TOTAL", "SAMPLE_PROP",
"CLUST_ZSCORE", "CLUST_PVALUE", "CLUST_QVALUE", "CLUST_EXC_CAUSE", "CLUST_COORDS",
"INTOGEN_DRIVER", "XREFS")
for gene in projdb.genes(join_xrefs=True, join_rec=True):
if gene.rec.sample_freq is not None and gene.rec.sample_freq > 0:
intogen_driver = 1 if sigdb.exists_gene(gene.id) else 0
write_line(gf, project_id, gene.id, gene.symbol, gene.fm_pvalue, gene.fm_qvalue, gene.fm_exc_cause,
gene.rec.sample_freq, total_samples, gene.rec.sample_prop or 0,
gene.clust_zscore, gene.clust_pvalue, gene.clust_qvalue, gene.clust_exc_cause,
gene.clust_coords, intogen_driver, ",".join(gene.xrefs))
log.info(" Pathways ...")
with ArcFile(task, arc, project_id, "pathways", "w") as pf:
write_line(pf, "PROJECT_ID", "PATHWAY_ID", "GENE_COUNT", "FM_ZSCORE", "FM_PVALUE", "FM_QVALUE",
"SAMPLE_FREQ", "SAMPLE_TOTAL", "SAMPLE_PROP", "GENE_FREQ", "GENE_TOTAL", "GENE_PROP")
for pathway in projdb.pathways(join_rec=True):
if pathway.rec.sample_freq is not None and pathway.rec.sample_freq > 0:
write_line(pf, project_id, pathway.id, pathway.gene_count, pathway.fm_zscore, pathway.fm_pvalue, pathway.fm_qvalue,
pathway.rec.sample_freq or 0, total_samples, pathway.rec.sample_prop or 0,
pathway.rec.gene_freq or 0, pathway.gene_count, pathway.rec.gene_prop or 0)
if not config.skip_oncodrivefm:
log.info(" Genes per sample functional impact ...")
with ArcFile(task, arc, project_id, "fimpact.gitools.tdm", "w") as f:
write_line(f, "SAMPLE", "GENE_ID",
"SIFT_SCORE", "SIFT_TRANSFIC", "SIFT_TRANSFIC_CLASS",
"PPH2_SCORE", "PPH2_TRANSFIC", "PPH2_TRANSFIC_CLASS",
"MA_SCORE", "MA_TRANSFIC", "MA_TRANSFIC_CLASS")
for fields in projdb.sample_gene_fimpacts():
(gene, sample,
sift_score, sift_tfic, sift_tfic_class,
pph2_score, pph2_tfic, pph2_tfic_class,
ma_score, ma_tfic, ma_tfic_class) = fields
write_line(f, sample, gene,
sift_score, sift_tfic, TransFIC.class_name(sift_tfic_class),
pph2_score, pph2_tfic, TransFIC.class_name(pph2_tfic_class),
ma_score, ma_tfic, TransFIC.class_name(ma_tfic_class))
log.info("Saving project configuration ...")
with ArcFile(task, arc, project_id, "project", "w") as f:
names = ["PROJECT_ID", "ASSEMBLY", "SAMPLES_TOTAL"]
values = [project_id, project["assembly"], total_samples]
names, values = projres.get_annotations_to_save(config.project.annotations, project["annotations"], names=names, values=values)
tsv.write_line(f, *names)
tsv.write_line(f, *values, null_value="-")
finally:
if arc is not None:
arc.close()
projdb.close()
sigdb.close()
def liftover(project):
log = task.logger
conf = task.conf
config = GlobalConfig(conf)
lifted_project_port = task.ports("lifted_projects")
log.info("--- [{0}] --------------------------------------------".format(project["id"]))
log.info("Preparing liftOver files ...")
in_path = make_temp_file(task, suffix=".bed")
in_file = open(in_path, "w")
out_path = make_temp_file(task, suffix=".bed")
unmapped_path = os.path.join(project["temp_path"], "liftover_unmapped.bed")
projdb = ProjectDb(project["db"])
for var in projdb.variants(order_by="position"):
in_file.write(tsv.line_text("chr" + var.chr, var.start, var.start + len(var.ref), var.id))
in_file.close()
log.info("Running liftOver ...")
project["from_assembly"] = project["assembly"]
project["assembly"] = "hg19"
cmd = " ".join(
[
conf["liftover_bin"],
in_path,
os.path.join(conf["liftover_chain_path"], "hg18ToHg19.over.chain"),
out_path,
unmapped_path,
]
)
log.debug(cmd)
subprocess.call(cmd, shell=True)
log.info("Annotating unmapped variants ...")
count = 0
with open(unmapped_path, "r") as f:
for line in f:
if line.lstrip().startswith("#"):
continue
fields = line.rstrip().split("\t")
var_id = int(fields[3])
projdb.update_variant_start(var_id, start=None)
count += 1
log.info(" {0} unmapped variants annotated".format(count))
log.info("Updating variants ...")
count = 0
with open(out_path, "r") as f:
for line in f:
fields = line.rstrip().split("\t")
chr, start, end, var_id = fields
projdb.update_variant_start(var_id, start=start)
count += 1
log.info(" {0} variants".format(count))
remove_temp(task, in_path, out_path)
projdb.commit()
projdb.close()
lifted_project_port.send(project)
