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[pygenomeworks] Fix counts of incorrect starts and ends in evaluate_paf #562

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merged 4 commits into from
Sep 22, 2020
Merged

[pygenomeworks] Fix counts of incorrect starts and ends in evaluate_paf #562

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925edca
[pygenomeworks] Fix incorrect output of number of mismatched starts/ends
edawson Sep 16, 2020
a47641f
[pygenomeworks] Add tabulation for mismatched starts/ends to target a…
edawson Sep 16, 2020
b3b0a65
[pygenomeworks] Remove commented out code from evaluate_paf.
edawson Sep 21, 2020
cc09756
Merge branch 'dev-v0.6.0' into paf-compare
edawson Sep 21, 2020
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68 changes: 41 additions & 27 deletions pygenomeworks/bin/evaluate_paf
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Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,8 @@ def match_overlaps(record, other, pos_tolerance, min_reciprocal_overlap):
"""

equal, query_start_valid, query_end_valid, target_start_valid, target_end_valid, strands_equal = records_equal(record, other, pos_tolerance)

reciprocal = calculate_reciprocal_overlap(record, other) > min_reciprocal_overlap
pct_recip = calculate_reciprocal_overlap(record, other)
reciprocal = pct_recip > min_reciprocal_overlap

match = equal or reciprocal

Expand All @@ -100,6 +100,7 @@ def match_overlaps(record, other, pos_tolerance, min_reciprocal_overlap):
"target_start_valid": target_start_valid,
"target_end_valid": target_end_valid,
"reciprocal_overlaps": reciprocal,
"percent_reciprocal": pct_recip,
"strands_equal" : strands_equal,
"equal" : equal,
"match": match}
Expand Down Expand Up @@ -175,69 +176,82 @@ def evaluate_paf(truth_paf_filepath, test_paf_filepath, pos_tolerance, min_recip
(test_overlap.query_sequence_name == test_overlap.target_sequence_name):
continue
test_overlap_count += 1
# query_0 = (test_overlap.query_start, test_overlap.query_end)
# target_0 = (test_overlap.target_start, test_overlap.target_end)

key = generate_key(test_overlap.query_sequence_name, test_overlap.target_sequence_name)
key_reversed = generate_key(test_overlap.target_sequence_name, test_overlap.query_sequence_name)

# if (key in seen_test_overlap_keys) or (key_reversed in seen_test_overlap_keys):
# continue

# seen_test_overlap_keys.add(key)
# seen_test_overlap_keys.add(key_reversed)

best_pct_match = 0.0
best_ends = [1, 1, 1, 1]

found_match = False
if key in truth_keys:
for truth_interval in truth_query_intervals[test_overlap.query_sequence_name]:
truth_overlap = truth_interval.data
match_statistics = match_overlaps(truth_overlap, test_overlap, pos_tolerance, min_reciprocal)
incorrect_query_start += not match_statistics["query_start_valid"]
incorrect_query_end += not match_statistics["query_end_valid"]
incorrect_target_start += not match_statistics["target_start_valid"]
incorrect_target_end += not match_statistics["target_end_valid"]
if match_statistics["match"]:
true_positive_count += 1
found_match = True
best_pct_match = match_statistics["percent_reciprocal"]
best_ends = [0, 0, 0, 0]
break
pct_match = match_statistics["percent_reciprocal"]
if pct_match > best_pct_match:
best_pct_match = pct_match
best_ends[0] = 1 if not match_statistics["query_start_valid"] else 0
best_ends[1] = 1 if not match_statistics["query_end_valid"] else 0
best_ends[2] = 1 if not match_statistics["target_start_valid"] else 0
best_ends[3] = 1 if not match_statistics["target_end_valid"] else 0
if not found_match:
for truth_interval in truth_target_intervals[test_overlap.target_sequence_name]:
truth_overlap = truth_interval.data
match_statistics = match_overlaps(truth_overlap, test_overlap, pos_tolerance, min_reciprocal)
incorrect_query_start += not match_statistics["query_start_valid"]
incorrect_query_end += not match_statistics["query_end_valid"]
incorrect_target_start += not match_statistics["target_start_valid"]
incorrect_target_end += not match_statistics["target_end_valid"]
if match_statistics["match"]:
true_positive_count += 1
found_match = True
break
pct_match = match_statistics["percent_reciprocal"]
if pct_match > best_pct_match:
best_pct_match = pct_match
best_ends[0] = 1 if not match_statistics["query_start_valid"] else 0
best_ends[1] = 1 if not match_statistics["query_end_valid"] else 0
best_ends[2] = 1 if not match_statistics["target_start_valid"] else 0
best_ends[3] = 1 if not match_statistics["target_end_valid"] else 0
if not found_match and key_reversed in truth_keys:
test_overlap = reverse_record(test_overlap)
for truth_interval in truth_query_intervals[key_reversed]:
truth_overlap = truth_interval.data
match_statistics = match_overlaps(truth_overlap, test_overlap)
incorrect_query_start += not match_statistics["query_start_valid"]
incorrect_query_end += not match_statistics["query_end_valid"]
incorrect_target_start += not match_statistics["target_start_valid"]
incorrect_target_end += not match_statistics["target_end_valid"]
if match_statistics["match"]:
true_positive_count += 1
found_match = True
break
pct_match = match_statistics["percent_reciprocal"]
if pct_match > best_pct_match:
best_pct_match = pct_match
best_ends[0] = 1 if not match_statistics["query_start_valid"] else 0
best_ends[1] = 1 if not match_statistics["query_end_valid"] else 0
best_ends[2] = 1 if not match_statistics["target_start_valid"] else 0
best_ends[3] = 1 if not match_statistics["target_end_valid"] else 0
if not found_match:
for truth_interval in truth_target_intervals[key_reversed]:
truth_overlap = truth_interval.data
match_statistics = match_overlaps(truth_overlap, test_overlap)
incorrect_query_start += not match_statistics["query_start_valid"]
incorrect_query_end += not match_statistics["query_end_valid"]
incorrect_target_start += not match_statistics["target_start_valid"]
incorrect_target_end += not match_statistics["target_end_valid"]
if match_statistics["match"]:
true_positive_count += 1
found_match = True
break

pct_match = match_statistics["percent_reciprocal"]
if pct_match > best_pct_match:
best_pct_match = pct_match
best_ends[0] = 1 if not match_statistics["query_start_valid"] else 0
best_ends[1] = 1 if not match_statistics["query_end_valid"] else 0
best_ends[2] = 1 if not match_statistics["target_start_valid"] else 0
best_ends[3] = 1 if not match_statistics["target_end_valid"] else 0
incorrect_query_start += best_ends[0]
incorrect_query_end += best_ends[1]
incorrect_target_start += best_ends[2]
incorrect_target_end += best_ends[3]

if not found_match:
false_positive_count += 1

Expand Down