[med-svn] [Git][med-team/q2-longitudinal][upstream] New upstream version 2023.9.1+ds
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 30 19:16:58 GMT 2024
Andreas Tille pushed to branch upstream at Debian Med / q2-longitudinal
Commits:
fe408595 by Andreas Tille at 2024-01-30T20:09:10+01:00
New upstream version 2023.9.1+ds
- - - - -
28 changed files:
- LICENSE
- ci/recipe/meta.yaml
- q2_longitudinal/__init__.py
- + q2_longitudinal/_examples.py
- q2_longitudinal/_format.py
- q2_longitudinal/_longitudinal.py
- q2_longitudinal/_transformer.py
- q2_longitudinal/_type.py
- q2_longitudinal/_utilities.py
- q2_longitudinal/_vega_specs/__init__.py
- q2_longitudinal/_vega_specs/volatility/__init__.py
- q2_longitudinal/_vega_specs/volatility/axis.py
- q2_longitudinal/_vega_specs/volatility/const.py
- q2_longitudinal/_vega_specs/volatility/data.py
- q2_longitudinal/_vega_specs/volatility/legend.py
- q2_longitudinal/_vega_specs/volatility/mark.py
- q2_longitudinal/_vega_specs/volatility/render.py
- q2_longitudinal/_vega_specs/volatility/scale.py
- q2_longitudinal/_vega_specs/volatility/signal.py
- q2_longitudinal/plugin_setup.py
- q2_longitudinal/tests/__init__.py
- + q2_longitudinal/tests/data/ecam-sample-md-blanks.tsv
- + q2_longitudinal/tests/data/ecam_map_maturity_nans.txt
- q2_longitudinal/tests/test_format.py
- q2_longitudinal/tests/test_longitudinal.py
- q2_longitudinal/tests/test_transformer.py
- q2_longitudinal/tests/test_type.py
- setup.py
Changes:
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2017-2021, QIIME 2 development team.
+Copyright (c) 2017-2023, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
ci/recipe/meta.yaml
=====================================
@@ -18,19 +18,19 @@ requirements:
run:
- python {{ python }}
- - numpy
+ - numpy {{ numpy }}
- pandas {{ pandas }}
- - scipy >=1.5
+ - scipy {{ scipy }}
- statsmodels >=0.9.0
- - patsy
- - scikit-bio >=0.5.5
- - seaborn
+ - patsy {{ patsy }}
+ - scikit-bio {{ scikit_bio }}
+ - seaborn {{ seaborn }}
- qiime2 {{ qiime2_epoch }}.*
- q2-types {{ qiime2_epoch }}.*
- q2-sample-classifier {{ qiime2_epoch }}.*
- q2templates {{ qiime2_epoch }}.*
- q2-feature-table {{ qiime2_epoch }}.*
- - matplotlib
+ - matplotlib {{ matplotlib }}
test:
requires:
@@ -45,6 +45,9 @@ test:
- q2_longitudinal
- qiime2.plugins.longitudinal
+ commands:
+ - py.test --pyargs q2_longitudinal
+
about:
home: https://qiime2.org
license: BSD-3-Clause
=====================================
q2_longitudinal/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_examples.py
=====================================
@@ -0,0 +1,42 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2017-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import os
+import pkg_resources
+
+import qiime2
+
+
+def _get_data_from_tests(path):
+ return pkg_resources.resource_filename('q2_longitudinal.tests',
+ os.path.join('data', path))
+
+
+def sample_md_blanks_factory():
+ return qiime2.Metadata.load(
+ _get_data_from_tests('ecam-sample-md-blanks.tsv')
+ )
+
+
+def longitudinal_volatility(use):
+ metadata = use.init_metadata('metadata', sample_md_blanks_factory)
+
+ volatility_viz, = use.action(
+ use.UsageAction('longitudinal', 'volatility'),
+ use.UsageInputs(
+ metadata=metadata,
+ state_column='month'
+ ),
+ use.UsageOutputNames(
+ visualization='volatility_plot'
+ )
+ )
+ # This is testing the expected behavior for _convert_nan_to_none()
+ # Assuring us that NaNs are successfully converted to nulls in the viz
+ volatility_viz.assert_has_line_matching('index.html',
+ r'^\s*"month": null,$')
=====================================
q2_longitudinal/_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_longitudinal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -44,7 +44,9 @@ def pairwise_differences(output_dir: str, metadata: qiime2.Metadata,
table: pd.DataFrame = None) -> None:
# find metric in metadata or derive from table and merge into metadata
- metadata = _add_metric_to_metadata(table, _load_metadata(metadata), metric)
+ metadata = _add_metric_to_metadata(table, _load_metadata(metadata,
+ group_column),
+ metric)
_validate_input_values(metadata, metric, individual_id_column,
group_column, state_column, state_1, state_2)
@@ -96,7 +98,7 @@ def pairwise_distances(output_dir: str, distance_matrix: skbio.DistanceMatrix,
palette: str = 'Set1',
replicate_handling: str = 'error',) -> None:
- metadata = _load_metadata(metadata)
+ metadata = _load_metadata(metadata, group_column)
_validate_input_values(metadata, None, individual_id_column, group_column,
state_column, state_1, state_2)
=====================================
q2_longitudinal/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_utilities.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -11,6 +11,7 @@ import os.path
import pkg_resources
from random import choice
import uuid
+import keyword
import numpy as np
from numpy.linalg.linalg import LinAlgError
@@ -310,25 +311,35 @@ def _per_method_pairwise_stats(groups, paired=False, parametric=True):
return result
+def _patsy_Q(term):
+ if not term.isidentifier() or keyword.iskeyword(term):
+ # the repr will ensure Python appropriate quotation for the string
+ return 'Q(%r)' % term
+ else:
+ return term
+
+
def _linear_effects(metadata, metric, state_column, group_columns,
individual_id_column, random_effects, formula):
+ state_column = _patsy_Q(state_column)
+ old_metric = metric
+ metric = _patsy_Q(metric)
+
# Assemble fixed_effects
if group_columns is not None:
- fixed_effects = [state_column] + group_columns
+ fixed_effects = [state_column] + [_patsy_Q(g) for g in group_columns]
else:
fixed_effects = [state_column]
# Assemble random_effects
if random_effects is not None:
# fit random slope to state_column
+ random_effects = [_patsy_Q(re) for re in random_effects]
random_effects = "~{0}".format(" + ".join(random_effects))
else:
# fit random intercept by default
random_effects = None
- # reformat terms to avoid patsy errors
- metadata, metric, old_metric = _dodge_patsy_errors(metadata, metric)
-
# format formula if one is not passed explicitly
if formula is None:
formula = "{0} ~ {1}".format(metric, " * ".join(fixed_effects))
@@ -430,9 +441,11 @@ def _multiple_tests_correction(df, method='fdr_bh'):
return df.sort_index()
-def _load_metadata(metadata):
+def _load_metadata(metadata, group_column=None):
metadata = metadata.to_dataframe()
metadata = metadata.apply(lambda x: pd.to_numeric(x, errors='ignore'))
+ if group_column is not None and group_column in metadata.columns:
+ metadata = metadata.dropna(subset=[group_column])
return metadata
@@ -801,6 +814,7 @@ def _summarize_feature_stats(table, state_md_col):
# df.fillna(None) does not work so used solution from:
# https://github.com/pandas-dev/pandas/issues/1972
def _convert_nan_to_none(df):
+ df = df.astype(object)
return df.where(pd.notnull(df), None)
@@ -859,22 +873,6 @@ def _parse_formula(formula):
return metric, group_columns
-def _dodge_patsy_errors(metadata, metric):
- # store original metric name to report in viz later
- old_metric = metric
- # semicolon-delimited taxonomies cause an error; copy to new metric column
- # also spaces and starting numeral (e.g., in feature name) cause error:
- # https://github.com/qiime2/q2-longitudinal/issues/101
- if ';' in metric or metric[0].isdigit() or ' ' in metric:
- # generate random column name but remove hyphens (patsy error)
- # and prepend word character (otherwise patsy splits strings starting
- # with numeral!)
- metric = 'f' + _generate_column_name(metadata).replace("-", "")
- metadata[metric] = metadata[old_metric]
-
- return metadata, metric, old_metric
-
-
def _importance_filtering(table, importances, importance_threshold,
feature_count):
'''
=====================================
q2_longitudinal/_vega_specs/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/axis.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/const.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/data.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/legend.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/mark.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/render.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/scale.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/_vega_specs/volatility/signal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -31,7 +31,7 @@ from ._longitudinal import (pairwise_differences, pairwise_distances,
maturity_index, feature_volatility,
plot_feature_volatility, anova)
import q2_longitudinal
-
+import q2_longitudinal._examples as ex
citations = Citations.load('citations.bib', package='q2_longitudinal')
@@ -319,7 +319,9 @@ plugin.visualizers.register_function(
'over time is co-plotted as "spaghetti" plots if the '
'"individual_id_column" parameter is used. state_column will '
'typically be a measure of time, but any numeric metadata column can '
- 'be used.')
+ 'be used.'),
+ examples={'longitudinal_volatility':
+ ex.longitudinal_volatility}
)
=====================================
q2_longitudinal/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/data/ecam-sample-md-blanks.tsv
=====================================
@@ -0,0 +1,877 @@
+sample-id anti-exposed-all day-of-life delivery diet diet-3 mom-or-child month month-of-life sex studyid
+#q2:types categorical numeric categorical categorical categorical categorical numeric numeric categorical categorical
+10249.C001.01SS n 0 Vaginal bd eb C 0 0 Female 1
+10249.C001.02SS n 36 Vaginal bd eb C 1.2 Female 1
+10249.C001.03SS n 42 Vaginal bd eb C 1.4 Female 1
+10249.C001.04SS y 49 Vaginal bd eb C 1.6 Female 1
+10249.C001.05SS y 57 Vaginal bd eb C 1.9 Female 1
+10249.C001.06SS y 61 Vaginal bd eb C 2 Female 1
+10249.C001.07SS y 92 Vaginal bd eb C 3 Female 1
+10249.C001.08SS y 122 Vaginal bd eb C 4 Female 1
+10249.C001.09SS y 153 Vaginal bd eb C 5 Female 1
+10249.C001.10SS y 183 Vaginal bd eb C 6 Female 1
+10249.C001.11SS y 214 Vaginal bd eb C 7 Female 1
+10249.C001.12SS y 244 Vaginal bd eb C 8 Female 1
+10249.C001.13SS y 273 Vaginal bd eb C 9 Female 1
+10249.C001.14SS y 294 Vaginal bd eb C 9.7 Female 1
+10249.C001.15SS y 300 Vaginal bd eb C 9.9 Female 1
+10249.C001.16SS y 307 Vaginal bd eb C 10.1 Female 1
+10249.C001.17SS y 337 Vaginal bd eb C 11.1 Female 1
+10249.C001.18SS y 367 Vaginal bd eb C 12.1 Female 1
+10249.C001.19SS y 375 Vaginal bd eb C 12.3 Female 1
+10249.C001.20SS y 378 Vaginal bd eb C 12.4 Female 1
+10249.C001.25SS y 411 Vaginal bd eb C 13.5 Female 1
+10249.C001.26SS y 427 Vaginal bd eb C 14 Female 1
+10249.C001.27SS y 435 Vaginal bd eb C 14.3 Female 1
+10249.C001.29SS y 488 Vaginal bd eb C 16 Female 1
+10249.C001.30SS y 551 Vaginal bd eb C 18.1 Female 1
+10249.C001.31SS y 613 Vaginal bd eb C 20.2 Female 1
+10249.C001.32SS y 677 Vaginal bd eb C 22 22.3 Female 1
+10249.C001.34SD y 733 Vaginal bd eb C 24 24.1 Female 1
+10249.C001.34SS y 733 Vaginal bd eb C 24 24.1 Female 1
+10249.C001.35SS y 792 Vaginal bd eb C 26 26 Female 1
+10249.C001.36SD y 855 Vaginal bd eb C 28 28.1 Female 1
+10249.C001.36SS y 855 Vaginal bd eb C 28 28.1 Female 1
+10249.C002.01SS n 0 Cesarean bd eb C 0 0 Male 2
+10249.C002.01SS.r n 0 Cesarean bd eb C 0 0 Male 2
+10249.C002.02SS n 32 Cesarean bd eb C 1 1.1 Male 2
+10249.C002.03SS n 53 Cesarean bd eb C 2 1.7 Male 2
+10249.C002.04SS n 60 Cesarean bd eb C 2 2 Male 2
+10249.C002.05SS n 89 Cesarean bd eb C 3 2.9 Male 2
+10249.C002.06SS n 123 Cesarean bd eb C 4 4 Male 2
+10249.C002.07SS n 158 Cesarean bd eb C 5 5.2 Male 2
+10249.C002.08SS n 190 Cesarean bd eb C 6 6.2 Male 2
+10249.C002.09SS n 249 Cesarean bd eb C 8 8.2 Male 2
+10249.C002.10SS n 284 Cesarean bd eb C 9 9.3 Male 2
+10249.C002.11SS n 315 Cesarean bd eb C 10 10.4 Male 2
+10249.C002.12SS n 338 Cesarean bd eb C 11 11.1 Male 2
+10249.C002.13SS n 369 Cesarean bd eb C 12 12.1 Male 2
+10249.C002.15SS n 488 Cesarean bd eb C 16 16 Male 2
+10249.C002.16SS n 555 Cesarean bd eb C 18 18.2 Male 2
+10249.C002.18SS n 678 Cesarean bd eb C 22 22.3 Male 2
+10249.C002.19SD n 731 Cesarean bd eb C 24 24 Male 2
+10249.C002.19SS n 731 Cesarean bd eb C 24 24 Male 2
+10249.C002.20SS n 798 Cesarean bd eb C 26 26.2 Male 2
+10249.C002.21SD n 856 Cesarean bd eb C 28 28.1 Male 2
+10249.C002.21SS n 856 Cesarean bd eb C 28 28.1 Male 2
+10249.C004.01SS n 0 Cesarean bd eb C 0 0 Male 4
+10249.C004.02SS n 31 Cesarean bd eb C 1 1 Male 4
+10249.C004.03SS n 55 Cesarean bd eb C 2 1.8 Male 4
+10249.C004.04SS n 91 Cesarean bd eb C 3 3 Male 4
+10249.C004.05SS n 124 Cesarean bd eb C 4 4.1 Male 4
+10249.C004.06SS n 154 Cesarean bd eb C 5 5.1 Male 4
+10249.C004.07SS n 186 Cesarean bd eb C 6 6.1 Male 4
+10249.C004.08SS n 214 Cesarean bd eb C 7 7 Male 4
+10249.C004.09SS y 245 Cesarean bd eb C 8 8.1 Male 4
+10249.C004.10SS y 257 Cesarean bd eb C 8 8.4 Male 4
+10249.C004.11SS y 266 Cesarean bd eb C 9 8.7 Male 4
+10249.C004.12SS y 278 Cesarean bd eb C 9 9.1 Male 4
+10249.C004.13SS y 308 Cesarean bd eb C 10 10.1 Male 4
+10249.C004.14SS y 340 Cesarean bd eb C 11 11.2 Male 4
+10249.C004.15SS y 366 Cesarean bd eb C 12 12 Male 4
+10249.C005.01SS n 1 Cesarean fd fd C 0 0 Female 5
+10249.C005.01SS.r n 1 Cesarean fd fd C 0 0 Female 5
+10249.C005.02SS n 29 Cesarean fd fd C 1 1 Female 5
+10249.C005.03SS n 43 Cesarean fd fd C 1 1.4 Female 5
+10249.C005.04SS n 63 Cesarean fd fd C 2 2.1 Female 5
+10249.C005.05SS n 93 Cesarean fd fd C 3 3.1 Female 5
+10249.C005.07SS n 155 Cesarean fd fd C 5 5.1 Female 5
+10249.C005.08SS n 183 Cesarean fd fd C 6 6 Female 5
+10249.C005.09SS n 213 Cesarean fd fd C 7 7 Female 5
+10249.C005.10SS n 245 Cesarean fd fd C 8 8.1 Female 5
+10249.C005.11SS n 276 Cesarean fd fd C 9 9.1 Female 5
+10249.C005.12SS n 304 Cesarean fd fd C 10 10 Female 5
+10249.C005.13SS n 332 Cesarean fd fd C 11 10.9 Female 5
+10249.C005.14SS n 367 Cesarean fd fd C 12 12.1 Female 5
+10249.C005.15SS n 428 Cesarean fd fd C 14 14.1 Female 5
+10249.C005.16SS n 485 Cesarean fd fd C 16 15.9 Female 5
+10249.C005.17SS n 549 Cesarean fd fd C 18 18 Female 5
+10249.C005.18SS n 612 Cesarean fd fd C 20 20.1 Female 5
+10249.C005.19SD n 667 Cesarean fd fd C 22 21.9 Female 5
+10249.C005.19SS n 667 Cesarean fd fd C 22 21.9 Female 5
+10249.C005.20SS n 735 Cesarean fd fd C 24 24.2 Female 5
+10249.C005.21SD n 793 Cesarean fd fd C 26 26.1 Female 5
+10249.C005.21SS n 793 Cesarean fd fd C 26 26.1 Female 5
+10249.C005.22SS n 855 Cesarean fd fd C 28 28.1 Female 5
+10249.C007.01SS n 1 Cesarean bd eb C 0 0 Male 7
+10249.C007.02SS n 30 Cesarean bd eb C 1 1 Male 7
+10249.C007.03SS n 49 Cesarean bd eb C 2 1.6 Male 7
+10249.C007.04SS n 66 Cesarean bd eb C 2 2.2 Male 7
+10249.C007.05SS n 93 Cesarean bd eb C 3 3.1 Male 7
+10249.C007.06SS n 127 Cesarean bd eb C 4 4.2 Male 7
+10249.C007.07SS n 155 Cesarean bd eb C 5 5.1 Male 7
+10249.C007.08SS n 183 Cesarean bd eb C 6 6 Male 7
+10249.C007.09SS y 214 Cesarean bd eb C 7 7 Male 7
+10249.C007.10SS y 219 Cesarean bd eb C 7 7.2 Male 7
+10249.C007.11SS y 243 Cesarean bd eb C 8 8 Male 7
+10249.C007.12SS y 258 Cesarean bd eb C 9 8.5 Male 7
+10249.C007.13SS y 266 Cesarean bd eb C 9 8.7 Male 7
+10249.C007.14SS y 274 Cesarean bd eb C 9 9 Male 7
+10249.C007.15SS y 303 Cesarean bd eb C 10 10 Male 7
+10249.C007.16SS y 334 Cesarean bd eb C 11 11 Male 7
+10249.C007.17SS y 364 Cesarean bd eb C 12 12 Male 7
+10249.C007.18SS y 427 Cesarean bd eb C 14 14 Male 7
+10249.C007.19SS y 490 Cesarean bd eb C 16 16.1 Male 7
+10249.C007.20SS y 551 Cesarean bd eb C 18 18.1 Male 7
+10249.C007.21SS y 608 Cesarean bd eb C 20 20 Male 7
+10249.C007.22SD y 669 Cesarean bd eb C 22 22 Male 7
+10249.C007.22SS y 669 Cesarean bd eb C 22 22 Male 7
+10249.C007.23SD y 729 Cesarean bd eb C 24 24 Male 7
+10249.C007.23SS y 729 Cesarean bd eb C 24 24 Male 7
+10249.C007.24SD y 793 Cesarean bd eb C 26 26.1 Male 7
+10249.C007.24SS y 793 Cesarean bd eb C 26 26.1 Male 7
+10249.C007.26SS y 853 Cesarean bd eb C 28 28 Male 7
+10249.C008.01SS n 1 Vaginal bd eb C 0 0 Male 8
+10249.C008.02SS n 31 Vaginal bd eb C 1 1 Male 8
+10249.C008.03SS n 72 Vaginal bd eb C 2 2.4 Male 8
+10249.C008.04SS n 126 Vaginal bd eb C 4 4.1 Male 8
+10249.C008.05SS n 159 Vaginal bd eb C 5 5.2 Male 8
+10249.C008.06SS y 189 Vaginal bd eb C 6 6.2 Male 8
+10249.C008.07SS y 194 Vaginal bd eb C 6 6.4 Male 8
+10249.C008.08SS y 212 Vaginal bd eb C 7 7 Male 8
+10249.C008.09SS y 250 Vaginal bd eb C 8 8.2 Male 8
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+10249.C047.02SS n 32 Cesarean bd eb C 1 1.1 Male 47
+10249.C047.05SS y 94 Cesarean bd eb C 3 3.1 Male 47
+10249.C047.06SD y 126 Cesarean bd eb C 4 4.1 Male 47
+10249.C047.06SS y 126 Cesarean bd eb C 4 4.1 Male 47
+10249.C047.07SD y 156 Cesarean bd eb C 5 5.1 Male 47
+10249.C047.07SS y 156 Cesarean bd eb C 5 5.1 Male 47
+10249.C047.08SD y 185 Cesarean bd eb C 6 6.1 Male 47
+10249.C047.08SS y 185 Cesarean bd eb C 6 6.1 Male 47
+10249.C047.09SS y 221 Cesarean bd eb C 7 7.3 Male 47
+10249.C047.10SS y 249 Cesarean bd eb C 8 8.2 Male 47
+10249.C047.11SS y 277 Cesarean bd eb C 9 9.1 Male 47
+10249.C047.13SS y 347 Cesarean bd eb C 11 11.4 Male 47
+10249.C049.01SS n 4 Vaginal bd bd C 0 0.1 Male 49
+10249.C049.02SD n 5 Vaginal bd bd C 0 0.2 Male 49
+10249.C049.02SS n 5 Vaginal bd bd C 0 0.2 Male 49
+10249.C049.03SD n 32 Vaginal bd bd C 1 1.1 Male 49
+10249.C049.03SS n 32 Vaginal bd bd C 1 1.1 Male 49
+10249.C049.04SS n 60 Vaginal bd bd C 2 2 Male 49
+10249.C049.07SD n 124 Vaginal bd bd C 4 4.1 Male 49
+10249.C049.07SS n 124 Vaginal bd bd C 4 4.1 Male 49
+10249.C049.08SD n 154 Vaginal bd bd C 5 5.1 Male 49
+10249.C049.08SS n 154 Vaginal bd bd C 5 5.1 Male 49
+10249.C049.09SD n 181 Vaginal bd bd C 6 6 Male 49
+10249.C049.09SS n 181 Vaginal bd bd C 6 6 Male 49
+10249.C049.10SS n 213 Vaginal bd bd C 7 7 Male 49
+10249.C049.11SS n 243 Vaginal bd bd C 8 8 Male 49
+10249.C049.12SS n 274 Vaginal bd bd C 9 9 Male 49
+10249.C049.13SS n 305 Vaginal bd bd C 10 10 Male 49
+10249.C049.14SS n 337 Vaginal bd bd C 11 11.1 Male 49
+10249.C052.02SS n 1 Vaginal bd eb C 0 0 Male 52
+10249.C052.03SD n 32 Vaginal bd eb C 1 1.1 Male 52
+10249.C052.03SS n 32 Vaginal bd eb C 1 1.1 Male 52
+10249.C052.04SD n 62 Vaginal bd eb C 2 2 Male 52
+10249.C052.04SS n 62 Vaginal bd eb C 2 2 Male 52
+10249.C052.05SD n 92 Vaginal bd eb C 3 3 Male 52
+10249.C052.06SS n 127 Vaginal bd eb C 4 4.2 Male 52
+10249.C052.07SS n 154 Vaginal bd eb C 5 5.1 Male 52
+10249.C052.08SS n 188 Vaginal bd eb C 6 6.2 Male 52
+10249.C052.09SS n 245 Vaginal bd eb C 8 8.1 Male 52
+10249.C053.02SD n 30 Cesarean bd bd C 1 1 Male 53
+10249.C053.02SS n 30 Cesarean bd bd C 1 1 Male 53
+10249.C053.03SD n 45 Cesarean bd bd C 2 1.5 Male 53
+10249.C053.03SS n 45 Cesarean bd bd C 2 1.5 Male 53
+10249.C053.04SD n 62 Cesarean bd bd C 2 2 Male 53
+10249.C053.04SS n 62 Cesarean bd bd C 2 2 Male 53
+10249.C053.05SD n 95 Cesarean bd bd C 3 3.1 Male 53
+10249.C053.05SS n 95 Cesarean bd bd C 3 3.1 Male 53
+10249.C053.06SS n 123 Cesarean bd bd C 4 4 Male 53
+10249.C053.07SS y 153 Cesarean bd bd C 5 5 Male 53
+10249.C053.08SS y 183 Cesarean bd bd C 6 6 Male 53
+10249.C053.09SS y 214 Cesarean bd bd C 7 7 Male 53
+10249.C055.01SS n 0 Cesarean fd fd C 0 0 Male 55
+10249.C055.02SD n 30 Cesarean fd fd C 1 1 Male 55
+10249.C055.02SS n 30 Cesarean fd fd C 1 1 Male 55
+10249.C055.03SD n 41 Cesarean fd fd C 1 1.3 Male 55
+10249.C055.03SS n 41 Cesarean fd fd C 1 1.3 Male 55
+10249.C055.04SD n 64 Cesarean fd fd C 2 2.1 Male 55
+10249.C055.04SS n 64 Cesarean fd fd C 2 2.1 Male 55
+10249.C055.05SD n 91 Cesarean fd fd C 3 3 Male 55
+10249.C055.05SS n 91 Cesarean fd fd C 3 3 Male 55
+10249.C055.06SS n 120 Cesarean fd fd C 4 3.9 Male 55
+10249.C055.07SS n 155 Cesarean fd fd C 5 5.1 Male 55
+10249.C055.08SS y 183 Cesarean fd fd C 6 6 Male 55
+10249.C055.09SS y 211 Cesarean fd fd C 7 6.9 Male 55
+10249.C056.01SS n 0 Cesarean bd bd C 0 0 Male 56
+10249.C056.02SS n 1 Cesarean bd bd C 0 0 Male 56
+10249.C056.03SD n 31 Cesarean bd bd C 1 1 Male 56
+10249.C056.03SS n 31 Cesarean bd bd C 1 1 Male 56
+10249.C056.04SD n 31 Cesarean bd bd C 1 1 Male 56
+10249.C056.04SS n 31 Cesarean bd bd C 1 1 Male 56
+10249.C056.05SD n 65 Cesarean bd bd C 2 2.1 Male 56
+10249.C056.05SS n 65 Cesarean bd bd C 2 2.1 Male 56
+10249.C056.06SS n 93 Cesarean bd bd C 3 3.1 Male 56
+10249.C056.07SS n 122 Cesarean bd bd C 4 4 Male 56
+10249.C056.08SS n 153 Cesarean bd bd C 5 5 Male 56
+10249.C056.09SS n 184 Cesarean bd bd C 6 6 Male 56
+10249.C056.10SS n 215 Cesarean bd bd C 7 7.1 Male 56
+10249.C057.02SS n 31 Cesarean bd eb C 1 1 Female 57
+10249.C057.03SD n 62 Cesarean bd eb C 2 2 Female 57
+10249.C057.03SS n 62 Cesarean bd eb C 2 2 Female 57
+10249.C057.04SD n 91 Cesarean bd eb C 3 3 Female 57
+10249.C057.04SS n 91 Cesarean bd eb C 3 3 Female 57
+10249.C057.05SD n 125 Cesarean bd eb C 4 4.1 Female 57
+10249.C057.05SS n 125 Cesarean bd eb C 4 4.1 Female 57
+10249.C057.06SS n 157 Cesarean bd eb C 5 5.2 Female 57
+10249.C057.08SS n 215 Cesarean bd eb C 7 7.1 Female 57
+10249.C057.09SS y 238 Cesarean bd eb C 8 7.8 Female 57
+10249.C057.10SS y 244 Cesarean bd eb C 8 8 Female 57
+10249.C057.11SS y 277 Cesarean bd eb C 9 9.1 Female 57
\ No newline at end of file
=====================================
q2_longitudinal/tests/data/ecam_map_maturity_nans.txt
=====================================
@@ -0,0 +1,879 @@
+#SampleID antiexposedall day_of_life delivery diet diet_3 mom_child month month_of_life sample_summary sex studyid observed_otus
+10249.C001.01SS n 0 Vaginal bd eb C 0 0 Vaginal.bd.n.0 Female 1 98
+10249.C001.02SS n 36 Vaginal bd eb C 1 1.2 Vaginal.bd.n.0 Female 1 27
+10249.C001.03SS n 42 Vaginal bd eb C 1 1.4 Vaginal.bd.n.0 Female 1 16
+10249.C001.04SS y 49 Vaginal bd eb C 2 1.6 Vaginal.bd.y.1 Female 1 17
+10249.C001.05SS y 57 Vaginal bd eb C 2 1.9 Vaginal.bd.y.1 Female 1 17
+10249.C001.06SS y 61 Vaginal bd eb C 2 2 Vaginal.bd.y.1 Female 1 14
+10249.C001.07SS y 92 Vaginal bd eb C 3 3 Vaginal.bd.y.1 Female 1 19
+10249.C001.08SS y 122 Vaginal bd eb C 4 4 Vaginal.bd.y.1 Female 1 18
+10249.C001.09SS y 153 Vaginal bd eb C 5 5 Vaginal.bd.y.1 Female 1 18
+10249.C001.10SS y 183 Vaginal bd eb C 6 6 Vaginal.bd.y.1 Female 1 23
+10249.C001.11SS y 214 Vaginal bd eb C 7 7 Vaginal.bd.y.1 Female 1 33
+10249.C001.12SS y 244 Vaginal bd eb C 8 8 Vaginal.bd.y.1 Female 1 31
+10249.C001.13SS y 273 Vaginal bd eb C 9 9 Vaginal.bd.y.1 Female 1 39
+10249.C001.14SS y 294 Vaginal bd eb C 10 9.7 Vaginal.bd.y.1 Female 1 12
+10249.C001.15SS y 300 Vaginal bd eb C 10 9.9 Vaginal.bd.y.1 Female 1 18
+10249.C001.16SS y 307 Vaginal bd eb C 10 10.1 Vaginal.bd.y.1 Female 1 30
+10249.C001.17SS y 337 Vaginal bd eb C 11 11.1 Vaginal.bd.y.1 Female 1 43
+10249.C001.18SS y 367 Vaginal bd eb C 12 12.1 Vaginal.bd.y.1 Female 1 61
+10249.C001.19SS y 375 Vaginal bd eb C 12 12.3 Vaginal.bd.y.1 Female 1 26
+10249.C001.20SS y 378 Vaginal bd eb C 12 12.4 Vaginal.bd.y.1 Female 1 26
+10249.C001.25SS y 411 Vaginal bd eb C 14 13.5 Vaginal.bd.y.1 Female 1 28
+10249.C001.26SS y 427 Vaginal bd eb C 14 14 Vaginal.bd.y.1 Female 1 38
+10249.C001.27SS y 435 Vaginal bd eb C 14 14.3 Vaginal.bd.y.1 Female 1 38
+10249.C001.29SS y 488 Vaginal bd eb C 16 16 Vaginal.bd.y.1 Female 1 52
+10249.C001.30SS y 551 Vaginal bd eb C 18 18.1 Vaginal.bd.y.1 Female 1 42
+10249.C001.31SS y 613 Vaginal bd eb C 20 20.2 Vaginal.bd.y.1 Female 1 56
+10249.C001.32SS y 677 Vaginal bd eb C 22 22.3 Vaginal.bd.y.1 Female 1 61
+10249.C001.34SD y 733 Vaginal bd eb C 24 24.1 Vaginal.bd.y.1 Female 1 62
+10249.C001.34SS y 733 Vaginal bd eb C 24 24.1 Vaginal.bd.y.1 Female 1 58
+10249.C001.35SS y 792 Vaginal bd eb C 26 26 Vaginal.bd.y.1 Female 1 66
+10249.C001.36SD y 855 Vaginal bd eb C 28 28.1 Vaginal.bd.y.1 Female 1 64
+10249.C001.36SS y 855 Vaginal bd eb C 28 28.1 Vaginal.bd.y.1 Female 1 71
+10249.C002.01SS n 0 Cesarean bd eb C 0 0 Cesarean.bd.n.1 Male 2 84
+10249.C002.01SS.r n 0 Cesarean bd eb C 0 0 Cesarean.bd.n.1 Male 2 53
+10249.C002.02SS n 32 Cesarean bd eb C 1 1.1 Cesarean.bd.n.1 Male 2 21
+10249.C002.03SS n 53 Cesarean bd eb C 2 1.7 Cesarean.bd.n.1 Male 2 10
+10249.C002.04SS n 60 Cesarean bd eb C 2 2 Cesarean.bd.n.1 Male 2 28
+10249.C002.05SS n 89 Cesarean bd eb C 3 2.9 Cesarean.bd.n.1 Male 2 11
+10249.C002.06SS n 123 Cesarean bd eb C 4 4 Cesarean.bd.n.1 Male 2 21
+10249.C002.07SS n 158 Cesarean bd eb C 5 5.2 Cesarean.bd.n.1 Male 2 14
+10249.C002.08SS n 190 Cesarean bd eb C 6 6.2 Cesarean.bd.n.1 Male 2 14
+10249.C002.09SS n 249 Cesarean bd eb C 8 8.2 Cesarean.bd.n.1 Male 2 18
+10249.C002.10SS n 284 Cesarean bd eb C 9 9.3 Cesarean.bd.n.1 Male 2 18
+10249.C002.11SS n 315 Cesarean bd eb C 10 10.4 Cesarean.bd.n.1 Male 2 23
+10249.C002.12SS n 338 Cesarean bd eb C 11 11.1 Cesarean.bd.n.1 Male 2 25
+10249.C002.13SS n 369 Cesarean bd eb C 12 12.1 Cesarean.bd.n.1 Male 2 27
+10249.C002.15SS n 488 Cesarean bd eb C 16 16 Cesarean.bd.n.1 Male 2 45
+10249.C002.16SS n 555 Cesarean bd eb C 18 18.2 Cesarean.bd.n.1 Male 2 57
+10249.C002.18SS n 678 Cesarean bd eb C 22 22.3 Cesarean.bd.n.1 Male 2 84
+10249.C002.19SD n 731 Cesarean bd eb C 24 24 Cesarean.bd.n.1 Male 2 84
+10249.C002.19SS n 731 Cesarean bd eb C 24 24 Cesarean.bd.n.1 Male 2 80
+10249.C002.20SS n 798 Cesarean bd eb C 26 26.2 Cesarean.bd.n.1 Male 2 67
+10249.C002.21SD n 856 Cesarean bd eb C 28 28.1 Cesarean.bd.n.1 Male 2 77
+10249.C002.21SS n 856 Cesarean bd eb C 28 28.1 Cesarean.bd.n.1 Male 2 81
+10249.C004.01SS n 0 Cesarean bd eb C 0 0 Cesarean.bd.n.1 Male 4 38
+10249.C004.02SS n 31 Cesarean bd eb C 1 1 Cesarean.bd.n.1 Male 4 13
+10249.C004.03SS n 55 Cesarean bd eb C 2 1.8 Cesarean.bd.n.1 Male 4 10
+10249.C004.04SS n 91 Cesarean bd eb C 3 3 Cesarean.bd.n.1 Male 4 16
+10249.C004.05SS n 124 Cesarean bd eb C 4 4.1 Cesarean.bd.n.1 Male 4 15
+10249.C004.06SS n 154 Cesarean bd eb C 5 5.1 Cesarean.bd.n.1 Male 4 13
+10249.C004.07SS n 186 Cesarean bd eb C 6 6.1 Cesarean.bd.n.1 Male 4 28
+10249.C004.08SS n 214 Cesarean bd eb C 7 7 Cesarean.bd.n.1 Male 4 21
+10249.C004.09SS y 245 Cesarean bd eb C 8 8.1 Cesarean.bd.y.1 Male 4 20
+10249.C004.10SS y 257 Cesarean bd eb C 8 8.4 Cesarean.bd.y.1 Male 4 22
+10249.C004.11SS y 266 Cesarean bd eb C 9 8.7 Cesarean.bd.y.1 Male 4 19
+10249.C004.12SS y 278 Cesarean bd eb C 9 9.1 Cesarean.bd.y.1 Male 4 19
+10249.C004.13SS y 308 Cesarean bd eb C 10 10.1 Cesarean.bd.y.1 Male 4 14
+10249.C004.14SS y 340 Cesarean bd eb C 11 11.2 Cesarean.bd.y.1 Male 4 28
+10249.C004.15SS y 366 Cesarean bd eb C 12 12 Cesarean.bd.y.1 Male 4 35
+10249.C005.01SS n 1 Cesarean fd fd C 0 0 Cesarean.fd.n.1 Female 5 75
+10249.C005.01SS.r n 1 Cesarean fd fd C 0 0 Cesarean.fd.n.1 Female 5 33
+10249.C005.02SS n 29 Cesarean fd fd C 1 1 Cesarean.fd.n.1 Female 5 15
+10249.C005.03SS n 43 Cesarean fd fd C 1 1.4 Cesarean.fd.n.1 Female 5 39
+10249.C005.04SS n 63 Cesarean fd fd C 2 2.1 Cesarean.fd.n.1 Female 5 42
+10249.C005.05SS n 93 Cesarean fd fd C 3 3.1 Cesarean.fd.n.1 Female 5 36
+10249.C005.07SS n 155 Cesarean fd fd C 5 5.1 Cesarean.fd.n.1 Female 5 34
+10249.C005.08SS n 183 Cesarean fd fd C 6 6 Cesarean.fd.n.1 Female 5 59
+10249.C005.09SS n 213 Cesarean fd fd C 7 7 Cesarean.fd.n.1 Female 5 38
+10249.C005.10SS n 245 Cesarean fd fd C 8 8.1 Cesarean.fd.n.1 Female 5 41
+10249.C005.11SS n 276 Cesarean fd fd C 9 9.1 Cesarean.fd.n.1 Female 5 47
+10249.C005.12SS n 304 Cesarean fd fd C 10 10 Cesarean.fd.n.1 Female 5 52
+10249.C005.13SS n 332 Cesarean fd fd C 11 10.9 Cesarean.fd.n.1 Female 5 51
+10249.C005.14SS n 367 Cesarean fd fd C 12 12.1 Cesarean.fd.n.1 Female 5 43
+10249.C005.15SS n 428 Cesarean fd fd C 14 14.1 Cesarean.fd.n.1 Female 5 59
+10249.C005.16SS n 485 Cesarean fd fd C 16 15.9 Cesarean.fd.n.1 Female 5 60
+10249.C005.17SS n 549 Cesarean fd fd C 18 18 Cesarean.fd.n.1 Female 5 54
+10249.C005.18SS n 612 Cesarean fd fd C 20 20.1 Cesarean.fd.n.1 Female 5 61
+10249.C005.19SD n 667 Cesarean fd fd C 22 21.9 Cesarean.fd.n.1 Female 5 67
+10249.C005.19SS n 667 Cesarean fd fd C 22 21.9 Cesarean.fd.n.1 Female 5 64
+10249.C005.20SS n 735 Cesarean fd fd C 24 24.2 Cesarean.fd.n.1 Female 5 63
+10249.C005.21SD n 793 Cesarean fd fd C 26 26.1 Cesarean.fd.n.1 Female 5 59
+10249.C005.21SS n 793 Cesarean fd fd C 26 26.1 Cesarean.fd.n.1 Female 5 65
+10249.C005.22SS n 855 Cesarean fd fd C 28 28.1 Cesarean.fd.n.1 Female 5 75
+10249.C007.01SS n 1 Cesarean bd eb C 0 0 Cesarean.bd.n.1 Male 7 107
+10249.C007.02SS n 30 Cesarean bd eb C 1 1 Cesarean.bd.n.1 Male 7 16
+10249.C007.03SS n 49 Cesarean bd eb C 2 1.6 Cesarean.bd.n.1 Male 7 30
+10249.C007.04SS n 66 Cesarean bd eb C 2 2.2 Cesarean.bd.n.1 Male 7 24
+10249.C007.05SS n 93 Cesarean bd eb C 3 3.1 Cesarean.bd.n.1 Male 7 27
+10249.C007.06SS n 127 Cesarean bd eb C 4 4.2 Cesarean.bd.n.1 Male 7 18
+10249.C007.07SS n 155 Cesarean bd eb C 5 5.1 Cesarean.bd.n.1 Male 7 23
+10249.C007.08SS n 183 Cesarean bd eb C 6 6 Cesarean.bd.n.1 Male 7 25
+10249.C007.09SS y 214 Cesarean bd eb C 7 7 Cesarean.bd.y.1 Male 7 16
+10249.C007.10SS y 219 Cesarean bd eb C 7 7.2 Cesarean.bd.y.1 Male 7 18
+10249.C007.11SS y 243 Cesarean bd eb C 8 8 Cesarean.bd.y.1 Male 7 18
+10249.C007.12SS y 258 Cesarean bd eb C 9 8.5 Cesarean.bd.y.1 Male 7 20
+10249.C007.13SS y 266 Cesarean bd eb C 9 8.7 Cesarean.bd.y.1 Male 7 19
+10249.C007.14SS y 274 Cesarean bd eb C 9 9 Cesarean.bd.y.1 Male 7 15
+10249.C007.15SS y 303 Cesarean bd eb C 10 10 Cesarean.bd.y.1 Male 7 38
+10249.C007.16SS y 334 Cesarean bd eb C 11 11 Cesarean.bd.y.1 Male 7 31
+10249.C007.17SS y 364 Cesarean bd eb C 12 12 Cesarean.bd.y.1 Male 7 50
+10249.C007.18SS y 427 Cesarean bd eb C 14 14 Cesarean.bd.y.1 Male 7 65
+10249.C007.19SS y 490 Cesarean bd eb C 16 16.1 Cesarean.bd.y.1 Male 7 69
+10249.C007.20SS y 551 Cesarean bd eb C 18 18.1 Cesarean.bd.y.1 Male 7 83
+10249.C007.21SS y 608 Cesarean bd eb C 20 20 Cesarean.bd.y.1 Male 7 92
+10249.C007.22SD y 669 Cesarean bd eb C 22 22 Cesarean.bd.y.1 Male 7 79
+10249.C007.22SS y 669 Cesarean bd eb C 22 22 Cesarean.bd.y.1 Male 7 88
+10249.C007.23SD y 729 Cesarean bd eb C 24 24 Cesarean.bd.y.1 Male 7 92
+10249.C007.23SS y 729 Cesarean bd eb C 24 24 Cesarean.bd.y.1 Male 7 93
+10249.C007.24SD y 793 Cesarean bd eb C 26 26.1 Cesarean.bd.y.1 Male 7 85
+10249.C007.24SS y 793 Cesarean bd eb C 26 26.1 Cesarean.bd.y.1 Male 7 92
+10249.C007.26SS y 853 Cesarean bd eb C 28 28 Cesarean.bd.y.1 Male 7 91
+10249.C008.01SS n 1 Vaginal bd eb C 0 0 Vaginal.bd.n.0 Male 8 40
+10249.C008.02SS n 31 Vaginal bd eb C 1 1 Vaginal.bd.n.0 Male 8 21
+10249.C008.03SS n 72 Vaginal bd eb C 2 2.4 Vaginal.bd.n.0 Male 8 14
+10249.C008.04SS n 126 Vaginal bd eb C 4 4.1 Vaginal.bd.n.0 Male 8 41
+10249.C008.05SS n 159 Vaginal bd eb C 5 5.2 Vaginal.bd.n.0 Male 8 23
+10249.C008.06SS y 189 Vaginal bd eb C 6 6.2 Vaginal.bd.y.1 Male 8 19
+10249.C008.07SS y 194 Vaginal bd eb C 6 6.4 Vaginal.bd.y.1 Male 8 11
+10249.C008.08SS y 212 Vaginal bd eb C 7 7 Vaginal.bd.y.1 Male 8 15
+10249.C008.09SS y 250 Vaginal bd eb C 8 8.2 Vaginal.bd.y.1 Male 8 36
+10249.C008.10SS y 273 Vaginal bd eb C 9 9 Vaginal.bd.y.1 Male 8 45
+10249.C008.11SS y 308 Vaginal bd eb C 10 10.1 Vaginal.bd.y.1 Male 8 45
+10249.C008.12SS y 364 Vaginal bd eb C 12 12 Vaginal.bd.y.1 Male 8 54
+10249.C008.13SS y 437 Vaginal bd eb C 14 14.4 Vaginal.bd.y.1 Male 8 58
+10249.C008.14SS y 490 Vaginal bd eb C 16 16.1 Vaginal.bd.y.1 Male 8 71
+10249.C008.15SS y 552 Vaginal bd eb C 18 18.1 Vaginal.bd.y.1 Male 8 77
+10249.C008.16SD y 615 Vaginal bd eb C 20 20.2 Vaginal.bd.y.1 Male 8 78
+10249.C008.16SS y 615 Vaginal bd eb C 20 20.2 Vaginal.bd.y.1 Male 8 74
+10249.C008.18SS y 795 Vaginal bd eb C 26 26.1 Vaginal.bd.y.1 Male 8 111
+10249.C009.01SS n 1 Vaginal bd eb C 0 0 Vaginal.bd.n.0 Male 9 134
+10249.C009.02SS n 31 Vaginal bd eb C 1 1 Vaginal.bd.n.0 Male 9 11
+10249.C009.03SS n 64 Vaginal bd eb C 2 2.1 Vaginal.bd.n.0 Male 9 10
+10249.C009.04SS n 94 Vaginal bd eb C 3 3.1 Vaginal.bd.n.0 Male 9 8
+10249.C009.05SS n 122 Vaginal bd eb C 4 4 Vaginal.bd.n.0 Male 9 28
+10249.C009.06SS n 155 Vaginal bd eb C 5 5.1 Vaginal.bd.n.0 Male 9 37
+10249.C009.07SS n 185 Vaginal bd eb C 6 6.1 Vaginal.bd.n.0 Male 9 12
+10249.C009.08SS n 214 Vaginal bd eb C 7 7 Vaginal.bd.n.0 Male 9 15
+10249.C009.09SS n 246 Vaginal bd eb C 8 8.1 Vaginal.bd.n.0 Male 9 26
+10249.C009.10SS n 273 Vaginal bd eb C 9 9 Vaginal.bd.n.0 Male 9 31
+10249.C009.11SS n 305 Vaginal bd eb C 10 10 Vaginal.bd.n.0 Male 9 13
+10249.C009.12SS n 339 Vaginal bd eb C 11 11.1 Vaginal.bd.n.0 Male 9 36
+10249.C009.13SS n 366 Vaginal bd eb C 12 12 Vaginal.bd.n.0 Male 9 47
+10249.C009.14SS n 429 Vaginal bd eb C 14 14.1 Vaginal.bd.n.0 Male 9 53
+10249.C009.16SS n 555 Vaginal bd eb C 18 18.2 Vaginal.bd.n.0 Male 9 68
+10249.C009.17SS n 613 Vaginal bd eb C 20 20.2 Vaginal.bd.n.0 Male 9 71
+10249.C009.18SD n 681 Vaginal bd eb C 22 22.4 Vaginal.bd.n.0 Male 9 75
+10249.C009.18SS n 681 Vaginal bd eb C 22 22.4 Vaginal.bd.n.0 Male 9 71
+10249.C009.19SS n 739 Vaginal bd eb C 24 24.3 Vaginal.bd.n.0 Male 9 102
+10249.C009.20SD n 800 Vaginal bd eb C 26 26.3 Vaginal.bd.n.0 Male 9 55
+10249.C009.20SS n 800 Vaginal bd eb C 26 26.3 Vaginal.bd.n.0 Male 9 58
+10249.C009.21SS n 864 Vaginal bd eb C 28 28.4 Vaginal.bd.n.0 Male 9 79
+10249.C010.01SS n 2 Vaginal bd eb C 0 0.1 Vaginal.fd.n.0 Male 10 13
+10249.C010.01SS.r n 2 Vaginal bd eb C 0 0.1 Vaginal.fd.n.0 Male 10 15
+10249.C010.02SS n 30 Vaginal bd eb C 1 1 Vaginal.fd.n.0 Male 10 31
+10249.C010.03SS n 39 Vaginal bd eb C 1 1.3 Vaginal.fd.n.0 Male 10 13
+10249.C010.04SS n 43 Vaginal bd eb C 1 1.4 Vaginal.fd.n.0 Male 10 18
+10249.C010.05SS n 60 Vaginal bd eb C 2 2 Vaginal.fd.n.0 Male 10 24
+10249.C010.06SS n 93 Vaginal bd eb C 3 3.1 Vaginal.fd.n.0 Male 10 21
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+control3
=====================================
q2_longitudinal/tests/test_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/test_longitudinal.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -11,6 +11,7 @@ import unittest
from io import StringIO
from warnings import filterwarnings
import tempfile
+import re
import numpy as np
import pandas as pd
@@ -21,7 +22,7 @@ from qiime2.plugin.testing import TestPluginBase
from qiime2.plugins import longitudinal
from q2_longitudinal._utilities import (
- _get_group_pairs, _extract_distance_distribution,
+ _load_metadata, _get_group_pairs, _extract_distance_distribution,
_get_pairwise_differences, _validate_input_values, _validate_input_columns,
_between_subject_distance_distribution, _compare_pairwise_differences,
_multiple_group_difference, _per_method_pairwise_stats,
@@ -40,6 +41,20 @@ filterwarnings("ignore", category=RuntimeWarning)
class TestUtilities(TestPluginBase):
package = 'q2_longitudinal.tests'
+ def setUp(self):
+ super().setUp()
+
+ self.md_ecam_fp = qiime2.Metadata.load(
+ self.get_data_path('ecam_map_maturity.txt'))
+ self.md_ecam_nans_fp = qiime2.Metadata.load(
+ self.get_data_path('ecam_map_maturity_nans.txt'))
+
+ def test_load_metadata_group_nan_handling(self):
+ md_nans = _load_metadata(self.md_ecam_nans_fp, group_column='delivery')
+ md_no_nans = _load_metadata(self.md_ecam_fp, group_column='delivery')
+
+ self.assertTrue((md_nans.index == md_no_nans.index).all())
+
def test_get_group_pairs(self):
res, err = _get_group_pairs(
md, 'a', individual_id_column='ind', group_column='Group',
@@ -234,6 +249,8 @@ class TestLongitudinalPipelines(TestPluginBase):
self.md_ecam_fp = qiime2.Metadata.load(
self.get_data_path('ecam_map_maturity.txt'))
+ self.md_ecam_missing_fp = qiime2.Metadata.load(
+ self.get_data_path('ecam-sample-md-blanks.tsv'))
table_fp = self.get_data_path('ecam-table-maturity.qza')
self.table_ecam_fp = qiime2.Artifact.load(table_fp)
@@ -254,6 +271,39 @@ class TestLongitudinalPipelines(TestPluginBase):
state_column='diet', individual_id_column='studyid',
n_estimators=10)
+ # Testing updated _convert_nan_to_none() util method
+ # This confirms that any NaNs present in the data are converted to None
+ # json.dumps then converts these values to null
+ def test_longitudinal_volatility_missing_numerical_md(self):
+ volatility_viz = longitudinal.actions.volatility(
+ metadata=self.md_ecam_missing_fp,
+ state_column='month')
+ match_json = \
+ r'(?:<script id="spec" type="application/json">)' + \
+ r'([\s\S]*?)(?:</script>)'
+ # First group matches <script> from vega spec, non-capturing
+ # Secound group matches the vega JSON object within <script></script>
+ # Non-greedy match, so only matches one script element
+ # Third group matches </script>, also non-capturing
+
+ with tempfile.TemporaryDirectory() as temp_dir_name:
+ viz_fp = volatility_viz[0].save(os.path.join(temp_dir_name,
+ 'viz.qzv'))
+ extracted_fp = \
+ qiime2.sdk.Result.extract(viz_fp,
+ os.path.join(temp_dir_name, 'viz'))
+ index_fp = os.path.join(extracted_fp, 'data', 'index.html')
+
+ with open(index_fp, 'r') as fh:
+ regex_match = re.findall(match_json, fh.read())[0]
+
+ self.assertNotIn('NaN', regex_match)
+ self.assertNotIn('nan', regex_match)
+ self.assertIn('null', regex_match)
+
+ def test_examples(self):
+ self.execute_examples()
+
# This test class really just makes sure that each plugin runs without error.
# UtilitiesTests handles all stats under the hood, so here we just want to make
@@ -280,6 +330,8 @@ class TestLongitudinal(TestPluginBase):
self.table_taxa_fp = _load_features('ecam-table-small.qza')
self.md_ecam_fp = qiime2.Metadata.load(
self.get_data_path('ecam_map_maturity.txt'))
+ self.md_ecam_nans_fp = qiime2.Metadata.load(
+ self.get_data_path('ecam_map_maturity_nans.txt'))
self.md_ecam_dm = _load_dm('ecam-unweighted-distance-matrix.qza')
def test_validate_input_values(self):
@@ -356,6 +408,14 @@ class TestLongitudinal(TestPluginBase):
metric='e2c3ff4f647112723741aa72087f1bfa',
replicate_handling='drop')
+ def test_pairwise_differences_nan_group_column(self):
+ pairwise_differences(
+ output_dir=self.temp_dir.name, table=None,
+ metadata=self.md_ecam_nans_fp, group_column='delivery',
+ state_column='month', state_1=0, state_2=3,
+ individual_id_column='studyid', metric='observed_otus',
+ replicate_handling='drop')
+
def test_pairwise_distances(self):
pairwise_distances(
output_dir=self.temp_dir.name, distance_matrix=self.md_ecam_dm,
@@ -363,6 +423,13 @@ class TestLongitudinal(TestPluginBase):
state_column='month', state_1=0, state_2=3,
individual_id_column='studyid', replicate_handling='drop')
+ def test_pairwise_distances_nan_group_column(self):
+ pairwise_distances(
+ output_dir=self.temp_dir.name, distance_matrix=self.md_ecam_dm,
+ metadata=self.md_ecam_nans_fp, group_column='delivery',
+ state_column='month', state_1=0, state_2=3,
+ individual_id_column='studyid', replicate_handling='drop')
+
def test_linear_mixed_effects(self):
linear_mixed_effects(
output_dir=self.temp_dir.name, table=None,
=====================================
q2_longitudinal/tests/test_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_longitudinal/tests/test_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2021, QIIME 2 development team.
+# Copyright (c) 2017-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-longitudinal/-/commit/fe408595d91871392c7bd98d075f41647319dd42
--
View it on GitLab: https://salsa.debian.org/med-team/q2-longitudinal/-/commit/fe408595d91871392c7bd98d075f41647319dd42
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