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Fixes, mostly, the non assigned var
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This is pretty rough code

Essentially, I'm trying to ensure all variables (tree_a, tree_b, tree_a_pos, tree_a_neg, tree_b_pos, tree_b_neg) are initialized before use

Minimizing my desire to refactor this

[#15]
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@curtisim0
curtisim0 committed Aug 12, 2024
1 parent 28919dd commit 2454ad1
Showing 1 changed file with 37 additions and 83 deletions.
120 changes: 37 additions & 83 deletions cpt_intersect_adj/intersect_and_adjacent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,73 +84,40 @@ def intersect(a, b, window, stranding):
b_pos = []
tree_a = []
tree_b = []
if stranding == True:
for feat in rec_a_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue

for feat in rec_a_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue
interval = Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
if stranding:
if feat.strand > 0:
a_pos.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
a_pos.append(interval)
else:
a_neg.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
a_neg.append(interval)
else:
tree_a.append(interval)

for feat in rec_b_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue
for feat in rec_b_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue
interval = Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
if stranding:
if feat.strand > 0:
b_pos.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
b_pos.append(interval)
else:
b_neg.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
b_neg.append(interval)
else:
tree_b.append(interval)

else:
for feat in rec_a_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue
tree_a.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
for feat in rec_b_i.features:
if feat.type == "remark" or feat.type == "annotation":
continue
tree_b.append(
Interval(
int(feat.location.start) - int(window),
int(feat.location.end) + int(window),
feat.id,
)
)
if stranding:
# builds interval tree from Interval objects of form (start, end, id) for each feature
# tree_a = IntervalTree(list(treeFeatures_noRem(rec_a_i.features, window)))
# tree_b = IntervalTree(list(treeFeatures_noRem(rec_b_i.features, window)))
# else:
tree_a_pos = IntervalTree(a_pos)
tree_a_neg = IntervalTree(a_neg)
tree_b_pos = IntervalTree(b_pos)
Expand All @@ -167,61 +134,48 @@ def intersect(a, b, window, stranding):
rec_b_hits_in_a = []

for feature in rec_a_i.features:
# Save each feature in rec_a that overlaps a feature in rec_b
# hits = tree_b.find_range((int(feature.location.start), int(feature.location.end)))

if feature.type == "remark" or feature.type == "annotation":
continue

if stranding == False:
if not stranding:
hits = tree_b[
int(feature.location.start) : int(feature.location.end)
]

# feature id is saved in interval result.data, use map to get full feature
for hit in hits:
rec_a_hits_in_b.append(rec_b_map[hit.data])

else:
if feature.strand > 0:
hits_pos = tree_b_pos[
hits = tree_b_pos[
int(feature.location.start) : int(feature.location.end)
]
for hit in hits_pos:
rec_a_hits_in_b.append(rec_b_map[hit.data])
else:
hits_neg = tree_b_neg[
hits = tree_b_neg[
int(feature.location.start) : int(feature.location.end)
]
for hit in hits_neg:
rec_a_hits_in_b.append(rec_b_map[hit.data])
for hit in hits:
rec_a_hits_in_b.append(rec_b_map[hit.data])

for feature in rec_b_i.features:
if feature.type == "remark" or feature.type == "annotation":
continue

if stranding == False:
if not stranding:
hits = tree_a[
int(feature.location.start) : int(feature.location.end)
]

# feature id is saved in interval result.data, use map to get full feature
for hit in hits:
rec_b_hits_in_a.append(rec_a_map[hit.data])

else:
if feature.strand > 0:
hits_pos = tree_a_pos[
hits = tree_a_pos[
int(feature.location.start) : int(feature.location.end)
]
for hit in hits_pos:
rec_b_hits_in_a.append(rec_a_map[hit.data])
else:
hits_neg = tree_a_neg[
hits = tree_a_neg[
int(feature.location.start) : int(feature.location.end)
]
for hit in hits_neg:
rec_b_hits_in_a.append(rec_a_map[hit.data])
for hit in hits:
rec_b_hits_in_a.append(rec_a_map[hit.data])

# Remove duplicate features using sets
rec_a_out.append(
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