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Dev min dist fix #25

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Dev min dist fix #25

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898dfaa
Merge pull request #22 from phac-nml/dev
sgsutcliffe Jan 31, 2025
f4efdfb
removed unnecessary filtering of smaller distances
jrober84 Feb 17, 2025
24ec1cb
corrected issue of final file chunk not being processed
jrober84 Feb 17, 2025
4efe85e
corrected bug with not assigning addresses when first threshold fails
jrober84 Feb 18, 2025
2fb29bb
corrected issue of assignement with new cluster codes
jrober84 Feb 18, 2025
f027285
Merge dev
apetkau Feb 24, 2025
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2 changes: 0 additions & 2 deletions genomic_address_service/classes/assign.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ def __init__(self,dist_file,membership_file,threshold_map,linkage_method,address
self.assignments = {}
self.nomenclature_cluster_tracker = {}
self.query_ids = set()

if not linkage_method in self.avail_methods:
self.status = False
self.error_msgs.append(f'Provided {linkage_method} is not one of the accepted {self.avail_methods}')
Expand Down Expand Up @@ -221,7 +220,6 @@ def assign(self, n_records=1000,delim="\t"):
if value is None:
query_addr[idx] = self.nomenclature_cluster_tracker[rank_ids[idx]]
self.nomenclature_cluster_tracker[rank_ids[idx]]+=1

break

self.memberships_dict[qid] = ".".join([str(x) for x in query_addr])
10 changes: 6 additions & 4 deletions genomic_address_service/classes/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,9 @@ def read_pd(self):
continue
qid = line[0]
rid = line[1]

d = float(line[2])
#print(f'{qid} {rid} {d}')
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Guessing this a vestige of testing

if qid not in self.record_ids and len(self.dists) >= self.n_records:
self.sort_distances()
yield self.dists
Expand All @@ -69,6 +71,7 @@ def read_pd(self):
if d > self.max_dist:
continue
self.dists[qid][rid] = d
yield self.dists
self.sort_distances()


Expand All @@ -95,9 +98,6 @@ def read_matrix(self):
rid = self.header[i]
d = values[i]
if self.filter:
if self.min_dist is not None:
if d < self.min_dist:
continue
if self.max_dist is not None:
if d > self.max_dist:
continue
Expand All @@ -114,6 +114,7 @@ def read_data(self):
self.header = next(self.file_handle).split(self.delim)
elif ftype == 'parquet':
self.file_handle = ParquetFile(self.fpath)

if ftype == 'text' and dist_type == 'pd':
for chunk in self.read_pd():
if chunk is not None:
Expand All @@ -126,7 +127,8 @@ def read_data(self):
yield chunk
if chunk is None:
chunk = self.dists
yield chunk

return chunk



Expand Down