def update_db(project):
log = task.logger
conf = task.conf
projects_out_port = task.ports("projects_out")
project_id = project["id"]
log.info("--- [{0}] --------------------------------------------".format(project_id))
oclust = project["oncodriveclust"]
del project["oncodriveclust"]
if not os.path.exists(oclust["results"]):
log.warn("No results have been found. Skipping it.")
return
log.info("Updating the project database ...")
projdb = ProjectDb(project["db"])
exc_path = os.path.join(project["temp_path"], "oncodriveclust-excluded-cause.tsv")
log.info(" Excluded gene causes ...")
log.debug(" > {0}".format(exc_path))
count = 0
with tsv.open(exc_path, "r") as exf:
for gene, cause in tsv.lines(exf, (str, str), header=True):
projdb.update_gene(Gene(id=gene, clust_exc_cause=cause))
count += 1
log.debug(" {0} genes excluded".format(count))
log.info(" OncodriveCLUST results ...")
with tsv.open(oclust["results"], "r") as f:
types = (str, str, float, float, float)
columns = ("GENE", "CLUST_COORDS", "ZSCORE", "PVALUE", "QVALUE")
for gene, coords, zscore, pvalue, qvalue in tsv.lines(f, types, columns=columns, header=True, null_value="NA"):
projdb.update_gene(Gene(id=gene, clust_coords=coords, clust_zscore=zscore, clust_pvalue=pvalue,
clust_qvalue=qvalue, clust_exc_cause=ProjectDb.NO_GENE_EXC))
projdb.commit()
projdb.close()
projects_out_port.send(project)
def end():
log = task.logger
projects_out_port = task.ports("projects_out")
log.info("Updating the projects database ...")
for project_id, projects in task.context.items():
log.info("[{0}]".format(project_id))
for index, project in enumerate(projects):
projdb = ProjectDb(project["db"])
if index == 0:
log.info(" Functional impact ...")
projdb.delete_sample_gene_fimpact()
with tsv.open(project["sample_gene_fi_data"], "r") as f:
types = (int, str, float, float, int, float, float, int, float, float, int)
for fields in tsv.lines(f, types, header=True, null_value="-"):
projdb.add_sample_gene_fimpact(*fields)
ofm = project["oncodrivefm"]
del project["oncodrivefm"]
exc_path = os.path.join(project["temp_path"], "oncodrivefm-excluded-cause.tsv")
log.info(" Excluded gene causes ...")
log.debug(" > {0}".format(exc_path))
count = 0
with tsv.open(exc_path, "r") as exf:
for gene, cause in tsv.lines(exf, (str, str), header=True):
projdb.update_gene(Gene(id=gene, fm_exc_cause=cause))
count += 1
log.debug(" {0} genes excluded".format(count))
for feature, results_path in ofm:
log.info(" {0} ...".format(feature))
log.debug(" > {0}".format(results_path))
if feature == "genes":
with tsv.open(results_path, "r") as f:
count = 0
for gene, pvalue, qvalue in tsv.lines(f, (str, float, float), header=True):
projdb.update_gene(
Gene(id=gene, fm_pvalue=pvalue, fm_qvalue=qvalue, fm_exc_cause=ProjectDb.NO_GENE_EXC)
)
count += 1
log.info(" {0} genes".format(count))
elif feature == "pathways":
with tsv.open(results_path, "r") as f:
count = 0
for pathway, zscore, pvalue, qvalue in tsv.lines(f, (str, float, float, float), header=True):
projdb.update_pathway(
Pathway(id=pathway, fm_zscore=zscore, fm_pvalue=pvalue, fm_qvalue=qvalue)
)
count += 1
log.info(" {0} pathways".format(count))
projdb.commit()
projdb.close()
projects_out_port.send(projects[0])
