def create_from_file(self,
files={},
has_headers=False,
fields=[],
delimiter="\t",
process_file=True):
try:
folder = get_temporary_folder()
f = files["upload_file"]
bed_file = f
if process_file:
new_bed = os.path.join(folder, "new_bed.bed")
outfile = open(new_bed, "w")
if f.endswith(".gz"):
handle = gzip.open(f, "rt")
else:
handle = open(f)
lookup = app.config["GENOME_DATABASES"][self.db].get(
"ens_to_ucsc")
with handle as csvfile:
reader = csv.reader(csvfile, delimiter=delimiter)
for row in reader:
if reader.line_num == 1 and has_headers:
continue
out_arr = row[0:3]
if lookup:
out_arr[0] = lookup.get(out_arr[0], out_arr[0])
if len(fields) > 3:
for field in fields[3:]:
out_arr.append(row[field["position"] - 1])
outfile.write("\t".join(out_arr) + "\n")
outfile.close()
bed_file = new_bed
#reorder the fields
new_fields = []
for count, field in enumerate(fields[3:], start=1):
field["position"] = count
field["field"] = "f{}".format(count)
new_fields.append(field)
fields = new_fields
gz_bed = os.path.join(self.get_tracks_folder(),
"anno_{}.bed.gz".format(self.id))
os.system("sort -k1,1 -k2,2n {} | bgzip > {}".format(
bed_file, gz_bed))
os.system("tabix -p bed {}".format(gz_bed))
self.set_data("fields", fields)
self.set_data("bed_file", gz_bed)
self.set_data("processing_file", False)
self.update({"status": "complete"})
except Exception as e:
self.data["processing_file"] = False
app.logger.exception(
"Unable to create annotataions from file {}".format(f))
self.update({"status": "failed"})
def create_gene_set_from_remote_file(genome,
remote_location,
name,
description="",
make_default=False):
f_name = os.path.split(remote_location)[1]
folder = get_temporary_folder()
file_name = os.path.join(folder, f_name)
command = "wget '{}' -O {}".format(remote_location, file_name)
data = {"remote"}
os.system(command)
create_gene_set(genome, name, file_name, description, make_default)
shutil.rmtree(folder)
def create_from_remote_file(genome,
remote_location,
name,
type,
description=""):
f_name = os.path.split(remote_location)[1]
folder = get_temporary_folder()
file_name = os.path.join(folder, f_name)
command = "wget '{}' -O {}".format(remote_location, file_name)
data = {"remote"}
os.system(command)
create_annotation_set_from_bed(genome, file_name, type, name, description,
data)
shutil.rmtree(folder)
def create_node_thumbnail(tracks, images, config):
folder = config.get("folder")
if not folder:
folder = get_temporary_folder()
config["folder"] = folder
out_config = os.path.join(folder, "config.json")
config["images"] = images
json = ujson.dumps({"tracks": tracks, "config": config})
out = open(out_config, "w")
out.write(json)
out.close()
app_root = Path(app.root_path).parent
os.environ["NODE_PATH"] = "/usr/local/lib/node_modules"
cmd = "node {}/node/image_gen.js {}/config.json".format(app_root, folder)
os.system(cmd)
return folder
def create_from_avocato_output(self, output_dir=""):
self.set_data("remote_avacato_dir", output_dir)
remote_file = os.path.join(output_dir, "cell", "cell_all.csv")
tf = get_temporary_folder()
local_file = os.path.join(tf, "cell.csv")
remote_file = shlex.quote(remote_file)
os.system("wget {} -O {}".format(remote_file, local_file))
line_num = 0
headers = []
#work put headers
with open(local_file) as f:
for line in f:
arr = line.strip().split(",")
if line_num == 0:
for c, item in enumerate(arr, start=1):
headers.append({"name": item, "position": c})
line_num += 1
continue
if line_num == 1:
for c, item in enumerate(arr):
type = "text"
try:
int(item)
type = "integer"
except:
try:
float(item)
type = "double"
except:
pass
headers[c]["datatype"] = type
break
self.add_data_file(has_headers=True,
files={"upload_file": local_file},
fields=headers,
delimiter=",")
user = db.session.query(User).filter_by(id=self.owner).one()
send_email(user,
"Job Finished",
"job_finished",
url=self.get_url(external=True),
type="Avacato Visualisation")
def create_thumbnail_preview(db):
data = request.json
vs = ViewSet(db, data["viewset_id"])
folder = get_temporary_folder()
tn_det = data['thumbnail_details']
vs.data['thumbnail_details'] = tn_det
vs.data["margin"] = tn_det['margin']
vs.data["annotation_sets"] = data["annotations"]
tn = ThumbnailSet(db,
height=int(tn_det['height']),
width=int(tn_det['width']))
ids = list(range(1, 21))
gene_set = 0
if data.get("genes") and vs.db != "other":
gene_set = 1
tn.draw_view_set(vs, specific_views=ids, folder=folder, gene_set=gene_set)
images = []
url_folder = folder.replace("mlv", "")
for i_id in ids:
images.append("{}/tn{}.png".format(url_folder, i_id))
return ujson.dumps({"images": images, "success": True})
def create_test_thumbnails(db):
'''creates test thumbnails
'''
data = request.json
tracks = data.get("tracks")
#reverse the proxy
for track in tracks:
track['url'] = get_reverse_track_proxy(track['url'])
annotation_sets = data.get("annotations")
gene_set = data.get("genes")
if gene_set:
gene_set = 1
height = int(data.get("height", 100))
width = int(data.get("width", 200))
margin = int(data.get("margin", 0))
margin2 = int(data.get("margin2", 0))
#not yet implemented
region_length = int(data.get("region_length", 0))
region_length2 = int(data.get("region_length2", 0))
half_rl = int(region_length / 2)
half_rl2 = int(region_length2 / 2)
locations = data.get("locations")
double_view = data.get("double_view")
if double_view:
margin2 = margin + 10000
tn_set = ThumbnailSet(db,
tracks=tracks,
annotation_sets=annotation_sets,
gene_set=gene_set,
height=height,
width=width)
thumbnails = []
folder = get_temporary_folder()
url_folder = folder.replace("/mlv", "")
count = 1
for loc in locations:
tram_lines = [loc['start'], loc['end']]
if region_length:
middle = int((loc['end'] - loc['start']) / 2) + loc['start']
st = middle - half_rl
en = middle + half_rl
else:
st = loc['start'] - margin
en = loc['end'] + margin
stub = "tn" + str(count)
if not double_view:
tn_set.draw_thumbnail(loc['chr'],
st,
en,
folder,
stub,
tram_lines=tram_lines)
else:
if region_length:
middle = int((loc['end'] - loc['start']) / 2) + loc['start']
st = middle - half_rl
en = middle + half_rl
st2 = middle - half_rl2
en2 = middle + half_rl2
else:
st = loc['start'] - margin
en = loc['end'] + margin
st2 = loc['start'] - margin2
en2 = loc['end'] + margin2
views = [{
"chrom": loc['chr'],
"start": st,
"end": en,
'tram_lines': tram_lines
}, {
"chrom": loc['chr'],
"start": st2,
"end": en2,
'tram_lines': tram_lines
}]
tn_set.draw_composite_thumbnail(views, folder, stub)
thumbnails.append(os.path.join("/data", url_folder, stub + ".png"))
count += 1
return ujson.dumps(thumbnails)