tskit 1.0.0b2__cp313-cp313-win_amd64.whl → 1.0.1__cp313-cp313-win_amd64.whl
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- _tskit.cp313-win_amd64.pyd +0 -0
- tskit/_version.py +1 -1
- tskit/combinatorics.py +6 -0
- tskit/drawing.py +2 -4
- tskit/exceptions.py +8 -0
- tskit/genotypes.py +23 -20
- tskit/metadata.py +105 -1
- tskit/tables.py +1043 -493
- tskit/text_formats.py +4 -0
- tskit/trees.py +440 -261
- tskit/util.py +6 -7
- {tskit-1.0.0b2.dist-info → tskit-1.0.1.dist-info}/METADATA +8 -8
- tskit-1.0.1.dist-info/RECORD +27 -0
- {tskit-1.0.0b2.dist-info → tskit-1.0.1.dist-info}/WHEEL +1 -1
- tskit-1.0.0b2.dist-info/RECORD +0 -27
- {tskit-1.0.0b2.dist-info → tskit-1.0.1.dist-info}/entry_points.txt +0 -0
- {tskit-1.0.0b2.dist-info → tskit-1.0.1.dist-info}/licenses/LICENSE +0 -0
- {tskit-1.0.0b2.dist-info → tskit-1.0.1.dist-info}/top_level.txt +0 -0
tskit/text_formats.py
CHANGED
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@@ -119,6 +119,7 @@ def write_nexus(
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include_alignments,
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reference_sequence,
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missing_data_character,
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+
isolated_as_missing=None,
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):
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# See TreeSequence.write_nexus for documentation on parameters.
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if precision is None:
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@@ -154,6 +155,7 @@ def write_nexus(
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alignments = ts.alignments(
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reference_sequence=reference_sequence,
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missing_data_character=missing_data_character,
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+
isolated_as_missing=isolated_as_missing,
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)
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for u, alignment in zip(ts.samples(), alignments):
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print(2 * indent, f"n{u}", " ", alignment, sep="", file=out)
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@@ -196,6 +198,7 @@ def write_fasta(
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wrap_width,
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reference_sequence,
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missing_data_character,
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isolated_as_missing=None,
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):
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# See TreeSequence.write_fasta for documentation
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if wrap_width < 0 or int(wrap_width) != wrap_width:
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@@ -208,6 +211,7 @@ def write_fasta(
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alignments = ts.alignments(
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reference_sequence=reference_sequence,
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missing_data_character=missing_data_character,
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+
isolated_as_missing=isolated_as_missing,
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)
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for u, alignment in zip(ts.samples(), alignments):
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print(">", f"n{u}", sep="", file=output)
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