def do_GeneAnnotationWorker():
"""
This function starts the GeneAnnotationWorker/Manager combo
in order to add annotations for a set of upload genes in the POST
variable
"""
if request.method == 'POST':
file_obj = request.files['file']
filetype = request.form["filetype"]
filter_name = request.form["filter_name"]
filter_desc = request.form["filter_desc"]
if file_obj and allowed_file(file_obj.filename):
filename = secure_filename(file_obj.filename)
save_path = os.path.join(app.config['UPLOAD_FOLDER'], filename)
file_obj.save(save_path)
if filetype=='type_gene':
filter_mgr = filter_manager(db="test",conn=g.conn)
filter_mgr.create_filter(filter_name, filter_desc)
manager = annotation.GaussWorkerManager(db="test",conn=g.conn)
worker = annotation.GeneAnnotationWorker2("mygeneworker")
#manager.register_worker(worker)
manager.start_worker(worker, args=(filter_name,save_path))
flash("Job successfully queued", "success")
return redirect(url_for("filters"))
flash("Error in queueing job!", "error")
return redirect("/filters")
def get_variants(gene=None, sample_id=None, chrom=None, start=None, end=None):
"""
Flask function for variants endpoint. Sets up basic query string
which is passed in to the javascript datatables AJAX call.
"""
isoform = None
if sample_id is not None:
title = "%s" % sample_id
query_string = "sample_id=%s" % sample_id
elif gene is not None:
title = "<em>%s</em>" % gene
query_string = "gene=%s" % gene
elif chrom is not None:
chrom_int = int(chrom.lower().replace("chr",""))
title="%s: %s - %s" % (chrom, start, end)
query_string = "chrom=%s&start=%s&end=%s" % (chrom, start, end)
else:
title = 'All variants'
query_string = ""
filter_mgr = filter_manager(db="test",conn=g.conn)
filters = filter_mgr.get_all_filters()
return render_template("view_variants.html", title=Markup(title), query_string=Markup(query_string), filters=filters, isoform=isoform)
def jsonfilters():
"""
Returns jsonified list of filters for use in AJAX calls
and in modals that display current filters, etc
"""
filter_mgr = filter_manager(db="test",conn=g.conn)
rows = filter_mgr.get_all_filters()
return jsonify(result=[i for i in rows])
def filters():
"""
Show a list of current filters and user-defined/uploaded
sets.
"""
filter_mgr = filter_manager(db="test",conn=g.conn)
rows = filter_mgr.get_all_filters()
return render_template("filters.html", rows=rows, columns=["filter_name","description", "type", "date_added","color"])
def delete_filter(name):
"""
Delete a user-defined set. It is not possible to delete filters
defined by GAUSS
"""
filter_mgr = filter_manager(db="test",conn=g.conn)
filter_mgr.delete_filter(name)
# manager = annotation.GaussWorkerManager(db="test",conn=g.conn)
# worker = annotation.GeneAnnotationWorker2("mygeneworker")
# manager.register_worker(worker)
# manager.start_worker(worker, args=[filter_name]))
flash("Filter successfully deleted","success")
return redirect(url_for("filters"))
def __init__(self, db, conn):
super(GaussQuery, self).__init__()
self.db = db
self.conn = conn
self.var_mgr = variant_manager(db=self.db, conn=self.conn)
self.filter_mgr = filter_manager(db=self.db, conn=self.conn)
self.column_list = ["chrom", "start", "end", "sample_name", "id", "ref", "alt"]
self.custom_column_list = []
self.projection = {k: True for k in self.column_list}
#del self.projection["end"] # may not be necessary
self.projection["filter"] = True # can add to column_list?
self.projection["annotations.EFF"] = True # can add to column list?
self.grouped = False
self.skip = 0
self.limit = 1000
self.query = defaultdict(lambda: defaultdict(list))
