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topo link generation #87

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merged 1 commit into from
Nov 21, 2023
Merged

topo link generation #87

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19 changes: 15 additions & 4 deletions big_scape/comparison/binning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,8 @@ def generate_pairs(self, legacy_sorting=False) -> Generator[RecordPair, None, No
Generator[RegionPair]: Generator for Region pairs in this bin
"""
for record_a, record_b in combinations(self.source_records, 2):
if record_a.parent_gbk == record_b.parent_gbk:
continue
if legacy_sorting:
sorted_a, sorted_b = sorted((record_a, record_b), key=sort_name_key)
pair = RecordPair(sorted_a, sorted_b)
Expand Down Expand Up @@ -289,14 +291,16 @@ def generate_pairs(self, legacy_sorting=False) -> Generator[RecordPair, None, No
continue
self.done_record_ids.add(region._db_id)

for bgc_a in connected_reference_regions:
for bgc_b in singleton_reference_regions:
for region_a in connected_reference_regions:
for region_b in singleton_reference_regions:
if region_a.parent_gbk == region_b.parent_gbk:
continue
if legacy_sorting:
sorted_a, sorted_b = sorted((bgc_a, bgc_b), key=sort_name_key)
sorted_a, sorted_b = sorted((region_a, region_b), key=sort_name_key)
pair = RecordPair(sorted_a, sorted_b)

else:
pair = RecordPair(bgc_a, bgc_b)
pair = RecordPair(region_a, region_b)

yield pair

Expand Down Expand Up @@ -571,6 +575,9 @@ def generate_pairs(self, legacy_sorting=False) -> Generator[RecordPair, None, No
record_a = self.record_id_to_obj[record_a_id]
record_b = self.record_id_to_obj[record_b_id]

if record_a.parent_gbk == record_b.parent_gbk:
continue

if legacy_sorting:
sorted_a, sorted_b = sorted((record_a, record_b), key=sort_name_key)
pair = RecordPair(sorted_a, sorted_b)
Expand Down Expand Up @@ -630,6 +637,10 @@ def generate_pairs(self, legacy_sorting=False) -> Generator[RecordPair, None, No
existing_distances = set(DB.execute(select_statement).fetchall())

for pair in self.bin.generate_pairs(legacy_sorting):
# this should never happen, since no edges should be generated for
# records of the same parent gbk
if pair.record_a.parent_gbk == pair.record_b.parent_gbk:
continue
# if the pair is not in the set of existing distances, yield it
if (
pair.record_a._db_id,
Expand Down
24 changes: 0 additions & 24 deletions big_scape/comparison/legacy_workflow_alt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -313,30 +313,6 @@ def calculate_scores_pair(
for pair in pairs:
logging.debug(pair)
pair.comparable_region.log_comparable_region()
logging.debug("")
if pair.record_a.parent_gbk == pair.record_b.parent_gbk:
results.append(
(
pair.record_a._db_id,
pair.record_b._db_id,
0.0,
1.0,
1.0,
1.0,
edge_param_id,
pair.comparable_region.lcs_a_start,
pair.comparable_region.lcs_a_stop,
pair.comparable_region.lcs_b_start,
pair.comparable_region.lcs_b_stop,
pair.comparable_region.a_start,
pair.comparable_region.a_stop,
pair.comparable_region.b_start,
pair.comparable_region.b_stop,
pair.comparable_region.reverse,
)
)
continue

jaccard = calc_jaccard_pair(pair)

if jaccard == 0.0:
Expand Down
18 changes: 12 additions & 6 deletions big_scape/output/html_template/output/html_content/js/bigscape.js
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Original file line number Diff line number Diff line change
Expand Up @@ -327,12 +327,18 @@ function Bigscape(run_data, bs_data, bs_families, bs_alignment, bs_similarity, n
}
for (var a = 0; a < bs_data.length; a++) {
for (var b = 0; b < bs_data.length; b++) {
if ((a > b) && (bs_similarity[a][b] > intra_cutoff)) {
if ((bs_to_cl[a] !== bs_to_cl[b]) && (bs_similarity[a][b] < inter_cutoff)) {
continue;
// addind a topo link
if (bs_data[a]["hash"] == bs_data[b]["hash"]) {
graph.addLink(a, b, { weight: 0.01 });
}
else{
if ((a > b) && (bs_similarity[a][b] > intra_cutoff)) {
if ((bs_to_cl[a] !== bs_to_cl[b]) && (bs_similarity[a][b] < inter_cutoff)) {
continue;
}
var weight = bs_similarity[a][b];
graph.addLink(a, b, { weight: weight });
}
var weight = bs_similarity[a][b];
graph.addLink(a, b, { weight: weight });
}
}
}
Expand Down Expand Up @@ -450,7 +456,7 @@ function Bigscape(run_data, bs_data, bs_families, bs_alignment, bs_similarity, n
.attr("stroke-width", link["data"]["weight"] * 10);

if (graph.getNode(link.fromId).data.hash === graph.getNode(link.toId).data.hash) {
line = line.attr("stroke-dasharray", "10,10")
line = line.attr("stroke-dasharray", "10,10").attr("stroke-width", link["data"]["weight"] * 500);
}
return line
});
Expand Down
22 changes: 12 additions & 10 deletions test/comparison/test_binning.py
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Expand Up @@ -169,11 +169,11 @@ def test_num_pairs_correct_with_query_ref(self):
def test_legacy_sorting(self):
"""Tests whether the legacy sorting option in bin.pairs() correctly orders the pairs"""

gbk_a = GBK(Path("test1.gbk"), "test", "test")
gbk_a = GBK(Path("test1.gbk"), "test1", "test")
bgc_a = BGCRecord(gbk_a, 0, 0, 10, False, "")
gbk_b = GBK(Path("test2.gbk"), "test", "test")
gbk_b = GBK(Path("test2.gbk"), "test2", "test")
bgc_b = BGCRecord(gbk_b, 0, 0, 10, False, "")
gbk_c = GBK(Path("test3.gbk"), "test", "test")
gbk_c = GBK(Path("test3.gbk"), "test3", "test")
bgc_c = BGCRecord(gbk_c, 0, 0, 10, False, "")

# due to the order, this should generate a list of pairs as follows without legacy sort:
Expand Down Expand Up @@ -734,16 +734,18 @@ def test_cull_singletons_cutoff(self):
class TestMixComparison(TestCase):
def test_mix_iter(self):
"""Tests whether a new mix bin can be created for comparison"""
gbk = GBK(Path("test"), "test", source_type=bs_enums.SOURCE_TYPE.QUERY)
gbk1 = GBK(Path("test"), "test1", source_type=bs_enums.SOURCE_TYPE.QUERY)
gbk2 = GBK(Path("test"), "test2", source_type=bs_enums.SOURCE_TYPE.QUERY)
gbk3 = GBK(Path("test"), "test3", source_type=bs_enums.SOURCE_TYPE.QUERY)

bgc_a = BGCRecord(gbk, 0, 0, 10, False, "")
bgc_a.parent_gbk = gbk
bgc_a = BGCRecord(gbk1, 0, 0, 10, False, "")
bgc_a.parent_gbk = gbk1

bgc_b = BGCRecord(gbk, 0, 0, 10, False, "")
bgc_b.parent_gbk = gbk
bgc_b = BGCRecord(gbk2, 0, 0, 10, False, "")
bgc_b.parent_gbk = gbk2

bgc_c = BGCRecord(gbk, 0, 0, 10, False, "")
bgc_c.parent_gbk = gbk
bgc_c = BGCRecord(gbk3, 0, 0, 10, False, "")
bgc_c.parent_gbk = gbk3

bgc_list = [bgc_a, bgc_b, bgc_c]

Expand Down
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