def sizes(request):
"""Return chromosome sizes.
Retrieves the chromSiyes.tsv and either retrieves it as is or converts it
to a JSON format.
Args:
request: HTTP GET request object. The request can feature the following
queries:
id: id of the stored chromSizes [e.g.: hg19 or mm9]
type: return data format [tsv or json]
cum: return cumulative size or offset [0 or 1]
Returns:
A HTTP text or JSON response depending on the GET request.
A text response looks like this:
```
chr1 1
chr2 2
...
```
A JSON response looks like this:
```
{
chr1: {
size: 1,
offset: 0
}
chr2: {
size: 2,
offset: 1
},
...
}
```
"""
uuid = request.GET.get("id", False)
res_type = request.GET.get("type", "tsv")
incl_cum = request.GET.get("cum", False)
response = HttpResponse
is_json = False
if res_type == "json":
is_json = True
response = JsonResponse
if res_type != "json" and incl_cum:
return response(
"Sorry buddy. Cumulative sizes not yet supported for non-JSON "
"file types. 😞",
status=501,
)
# Try to find the db entry
try:
chrom_sizes = tm.Tileset.objects.get(uuid=uuid)
except Exception as e:
logger.exception(e)
err_msg = "Oh lord! ChromSizes for %s not found. 😬" % uuid
err_status = 404
if is_json:
return response({"error": err_msg}, status=err_status)
return response(err_msg, status=err_status)
# Try to load the chromosome sizes and return them as a list of
# (name, size) tuples
try:
if tgt.get_tileset_filetype(chrom_sizes) == "bigwig":
data = hgbi.chromsizes(chrom_sizes.datafile.path)
elif tgt.get_tileset_filetype(chrom_sizes) == "bigbed":
data = hgbb.chromsizes(chrom_sizes.datafile.path)
elif tgt.get_tileset_filetype(chrom_sizes) == "cooler":
data = tcs.get_cooler_chromsizes(chrom_sizes.datafile.path)
elif tgt.get_tileset_filetype(chrom_sizes) == "chromsizes-tsv":
data = tcs.get_tsv_chromsizes(chrom_sizes.datafile.path)
elif tgt.get_tileset_filetype(chrom_sizes) == "multivec":
data = tcs.get_multivec_chromsizes(chrom_sizes.datafile.path)
else:
data = ""
except Exception as ex:
logger.exception(ex)
err_msg = str(ex)
err_status = 500
if is_json:
return response({"error": err_msg}, status=err_status)
return response(err_msg, status=err_status)
# Convert the stuff if needed
try:
# data should be a list of (name, size) tuples coming
# coming and converted to a more appropriate data type
# going out
if res_type == "tsv":
lines = []
for (name, size) in data:
lines += ["{}\t{}\n".format(name, size)]
data = lines
if res_type == "json" and not incl_cum:
json_out = {}
for row in data:
json_out[row[0]] = {"size": int(row[1])}
data = json_out
if res_type == "json" and incl_cum:
json_out = {}
cum = 0
for row in data:
size = int(row[1])
json_out[row[0]] = {"size": size, "offset": cum}
cum += size
data = json_out
except Exception as e:
logger.exception(e)
err_msg = "THIS IS AN OUTRAGE!!!1! Something failed. 😡"
err_status = 500
if is_json:
return response({"error": err_msg}, status=err_status)
return response(err_msg, status=err_status)
return response(data)
def chromsizes(filename):
return hgbw.chromsizes(filename)