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authorArun Isaac2025-08-04 12:52:39 +0100
committerArun Isaac2025-08-06 22:40:41 +0100
commitbcdb235949c06db07172b0c6355a0059436b86fb (patch)
treeef2a4ab4ea6d3da60a894b50eb7a2470021852f1 /test-data/genotype3.tsv
parent2dc2efa7f77deb5ebcf7b80abefc162474614b2c (diff)
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Standardize file formats in the likeness of plink files.
* pyhegp/pyhegp.py: Import pandas.
(summary, pool, encrypt, cat): Use pandas data frames and new data
format.
* pyhegp/serialization.py: Import csv and pandas.
(Summary)[mean, std]: Delete fields.
[data]: New field.
(read_summary, write_summary, read_genotype, write_genotype): Use
pandas data frames and new data format.
* tests/test_serialization.py: Import column, columns and data_frames
from hypothesis.extra.pandas; pandas; negate from pyhegp.utils. Do not
import hypothesis.extra.numpy and approx from pytest.
(tabless_printable_ascii_text, chromosome_column, position_column,
reference_column, sample_names): New variables.
(summaries, genotype_reserved_column_name_p, genotype_frames): New
functions.
(test_read_write_summary_are_inverses): Use pandas data frames and new
data format.
(test_read_write_genotype_are_inverses): Use pandas for testing.
* doc/file-formats.md (File formats)[summary file]: Describe new
standard.
[genotype file]: New section.
* .guix/pyhegp-package.scm (pyhegp-package): Import python-pandas
from (gnu packages python-science).
(python-pyhegp)[propagated-inputs]: Add python-pandas.
* pyproject.toml (dependencies): Add pandas.
Diffstat (limited to 'test-data/genotype3.tsv')
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