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Handle floating point numbers in update_qai.py #1075

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merged 1 commit into from
Apr 12, 2024
Merged

Handle floating point numbers in update_qai.py #1075

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20 changes: 13 additions & 7 deletions micall/monitor/update_qai.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,10 +164,16 @@ def build_review_decisions(coverage_file, collated_counts_file, cascade_file,
# noinspection PyTypeChecker
sample_names = dict(map(itemgetter('tags', 'filename'), sample_sheet['DataSplit']))

def read_int(table, name):
ret = float(table[name])
if float(int(ret)) != ret:
raise ValueError(f"Bad value for {name!r}: {ret!r}. Expected an integer.")
return int(ret)

counts_map = {} # {tags: raw, (tags, seed): mapped]}
# sample,type,count
for counts in csv.DictReader(collated_counts_file):
count = int(counts['count'])
count = read_int(counts, 'count')
tags = sample_tags[counts['sample']]
count_type = counts['type']
if count_type not in ('raw', 'unmapped'):
Expand All @@ -178,11 +184,11 @@ def build_review_decisions(coverage_file, collated_counts_file, cascade_file,
unreported_tags = set()
for counts in csv.DictReader(cascade_file):
tags = sample_tags[counts['sample']]
counts_map[tags] = int(counts['demultiplexed']) * 2
counts_map[tags] = read_int(counts, 'demultiplexed') * 2
unreported_tags.add(tags)

key = tags, G2P_SEED_NAME
counts_map[key] = int(counts['v3loop']) * 2
counts_map[key] = read_int(counts, 'v3loop') * 2

sequencing_map = defaultdict(dict) # {tags: {project: sequencing}}
for sequencing in sequencings:
Expand All @@ -201,9 +207,9 @@ def build_review_decisions(coverage_file, collated_counts_file, cascade_file,
"tagged layouts missing?" % (tags, coverage_file.name))
sequencing = project_map.get(coverage['project'])
if sequencing is not None:
score = int(coverage['on.score'])
score = read_int(coverage, 'on.score')
else:
score = int(coverage['off.score'])
score = read_int(coverage, 'off.score')
first_project = sorted(project_map.keys())[0]
sequencing = project_map[first_project]
project_region_id = project_region_map[(coverage['project'],
Expand All @@ -226,8 +232,8 @@ def build_review_decisions(coverage_file, collated_counts_file, cascade_file,
'seed_region_id': seed_region_id,
'sample_name': coverage['sample'],
'score': score,
'min_coverage': int(coverage['min.coverage']),
'min_coverage_pos': int(coverage['which.key.pos']),
'min_coverage': read_int(coverage, 'min.coverage'),
'min_coverage_pos': read_int(coverage, 'which.key.pos'),
'raw_reads': raw_count,
'mapped_reads': mapped_count
}
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