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Fix bug in designation_helper.py when there are no children
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utils/designation_helper.py

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -12,10 +12,10 @@
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- Add alias json if necessary
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"""
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import typer
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import numpy as np
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import pandas as pd
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import typer
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from pango_aliasor.aliasor import Aliasor
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import numpy as np
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LINEAGE_NOTES = "lineage_notes.txt"
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LINEAGES_CSV = "lineages.csv"
@@ -110,16 +110,18 @@ def get_lineage_from_parent(parent_lineage: str):
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unaliased_parent = aliasor.uncompress(parent_lineage)
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# Filter to lineages descending from parent lineage
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children=unaliased[np.vectorize(lambda x: x.startswith(unaliased_parent))(unaliased)]
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children=unaliased[np.vectorize(lambda x: x.startswith(unaliased_parent + "."))(unaliased)]
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# Find number of levels of parent lineage
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parent_levels = unaliased_parent.count(".") + 1
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# Find numbers of level below parent lineage
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children_levels = np.vectorize(lambda x: extract_level(x, parent_levels))(children)
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# Find last entry of 1 level below parent lineage
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max_child = max(children_levels)
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if len(children) == 0:
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max_child = 0
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else:
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children_levels = np.vectorize(lambda x: extract_level(x, parent_levels))(children)
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# Find last entry of 1 level below parent lineage
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max_child = max(children_levels)
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# Create compressd child
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new_child_unaliased = f"{unaliased_parent}.{max_child+1}"

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