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DEV: update junction subpath calculations
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@Vini2
Vini2 committed Jul 1, 2024
1 parent de20b0c commit 256bc6f
Showing 1 changed file with 30 additions and 14 deletions.
44 changes: 30 additions & 14 deletions reneo/workflow/scripts/reneo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -605,7 +605,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
# Add subpaths
if juction_cov >= kwargs["mincov"]:
kwargs["logger"].debug(
f"Adding subpath {[u_index, final_vertex]}"
f"Adding subpath {[u_name, v_name]}"
)
subpaths[subpath_count] = [u_index, final_vertex]
subpath_count += 1
Expand All @@ -620,14 +620,18 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
u_pred_index = candidate_nodes.index(u_pred_name)
u_pred_cov = kwargs["unitig_coverages"][u_pred[:-1]]
u_cov = kwargs["unitig_coverages"][u[:-1]]
v_cov = kwargs["unitig_coverages"][v[:-1]]

if (
final_vertex != 0
and u_index != 0
and u_pred_index != final_vertex
):
kwargs["logger"].debug(
f"Coverage across - {u_pred}:{u_pred_cov}, {u}:{u_cov}, {v}:{v_cov}"
)
if (
abs(min(u_pred_cov, u_cov) - cov["weight"])
abs(min(u_pred_cov, u_cov) - min(u_cov, v_cov))
< kwargs["covtol"]
):
subpaths[subpath_count] = [
Expand All @@ -636,7 +640,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
final_vertex,
]
kwargs["logger"].debug(
f"Extending subpath based on predecessor coverage {[u_pred_index, u_index, final_vertex]}"
f"Extending subpath based on predecessor coverage {[u_pred, u, v]}, {[u_pred_cov, u_cov, v_cov]}"
)
subpath_count += 1

Expand All @@ -646,6 +650,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_succ_index = candidate_nodes.index(v_succ_name)
v_succ_cov = kwargs["unitig_coverages"][v_succ[:-1]]
v_cov = kwargs["unitig_coverages"][v[:-1]]
u_cov = kwargs["unitig_coverages"][u[:-1]]

if (
v_succ_index != 0
Expand All @@ -654,8 +659,11 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
and final_vertex != len(candidate_nodes)
and v_succ_index != u_index
):
kwargs["logger"].debug(
f"Coverage across - {u}:{u_cov}, {v}:{v_cov}, {v_succ}:{v_succ_cov}"
)
if (
abs(min(v_succ_cov, v_cov) - cov["weight"])
abs(min(v_succ_cov, v_cov) - min(u_cov, v_cov))
< kwargs["covtol"]
):
subpaths[subpath_count] = [
Expand All @@ -664,7 +672,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_succ_index,
]
kwargs["logger"].debug(
f"Extending subpath based on successor coverage {[u_index, final_vertex, v_succ_index]}"
f"Extending subpath based on successor coverage {[u, v, v_succ]}, {[u_cov, v_cov, v_succ_cov]}"
)
subpath_count += 1

Expand Down Expand Up @@ -696,7 +704,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
final_vertex,
]
kwargs["logger"].debug(
f"Extending subpath {[u_pred_index, u_index, final_vertex]}"
f"Extending subpath {[u_pred, u, v]}"
)
subpath_count += 1

Expand Down Expand Up @@ -724,7 +732,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_succ_index,
]
kwargs["logger"].debug(
f"Extending subpath {[u_index, final_vertex, v_succ_index]}"
f"Extending subpath {[u, v, v_succ]}"
)
subpath_count += 1

Expand Down Expand Up @@ -1025,7 +1033,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
# Add subpaths
if juction_cov >= kwargs["mincov"]:
kwargs["logger"].debug(
f"Adding subpath {[u_index, v_index]}"
f"Adding subpath {[u_name, v_name]}"
)
subpaths[subpath_count] = [u_index, v_index]
subpath_count += 1
Expand All @@ -1044,14 +1052,18 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
)
u_pred_cov = kwargs["unitig_coverages"][u_pred[:-1]]
u_cov = kwargs["unitig_coverages"][u[:-1]]
v_cov = kwargs["unitig_coverages"][v[:-1]]

if (
(v_index - 1) not in source_node_indices
and (u_index - 1) not in source_node_indices
and u_pred_index != v_index
):
kwargs["logger"].debug(
f"Coverage across - {u_pred}:{u_pred_cov}, {u}:{u_cov}, {v}:{v_cov}"
)
if (
abs(min(u_pred_cov, u_cov) - cov["weight"])
abs(min(u_pred_cov, u_cov) - min(u_cov, v_cov))
< kwargs["covtol"]
):
subpaths[subpath_count] = [
Expand All @@ -1060,7 +1072,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_index,
]
kwargs["logger"].debug(
f"Extending subpath based on predecessor coverage {[u_pred_index, u_index, v_index]}"
f"Extending subpath based on predecessor coverage {[u_pred, u, v]}, {[u_pred_cov, u_cov, v_cov]}"
)
subpath_count += 1

Expand All @@ -1074,6 +1086,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
)
v_succ_cov = kwargs["unitig_coverages"][v_succ[:-1]]
v_cov = kwargs["unitig_coverages"][v[:-1]]
u_cov = kwargs["unitig_coverages"][v[:-1]]

if (
(v_succ_index - 1) not in source_node_indices
Expand All @@ -1082,8 +1095,11 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
and (v_index - 1) not in sink_node_indices
and v_succ_index != u_index
):
kwargs["logger"].debug(
f"Coverage across - {u}:{u_cov}, {v}:{v_cov}, {v_succ}:{v_succ_cov}"
)
if (
abs(min(v_succ_cov, v_cov) - cov["weight"])
abs(min(v_succ_cov, v_cov) - min(u_cov, v_cov))
< kwargs["covtol"]
):
subpaths[subpath_count] = [
Expand All @@ -1092,7 +1108,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_succ_index,
]
kwargs["logger"].debug(
f"Extending subpath based on successor coverage {[u_index, v_index, v_succ_index]}"
f"Extending subpath based on successor coverage {[u, v, v_succ]}, {[u_cov, v_cov, v_succ_cov]}"
)
subpath_count += 1

Expand Down Expand Up @@ -1126,7 +1142,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_index,
]
kwargs["logger"].debug(
f"Extending subpath {[u_pred_index, u_index, v_index]}"
f"Extending subpath {[u_pred, u, v]}"
)
subpath_count += 1

Expand Down Expand Up @@ -1157,7 +1173,7 @@ def worker_resolve_components(component_queue, results_queue, **kwargs):
v_succ_index,
]
kwargs["logger"].debug(
f"Extending subpath {[u_index, v_index, v_succ_index]}"
f"Extending subpath {[u, v, v_succ]}"
)
subpath_count += 1

Expand Down

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