diff --git a/malariagen_data/af1.py b/malariagen_data/af1.py index 569b433f..5a4683d4 100644 --- a/malariagen_data/af1.py +++ b/malariagen_data/af1.py @@ -13,8 +13,8 @@ GCS_REGION_URLS = { "us-central1": "gs://vo_afun_release_master_us_central1", } -XPEHH_GWSS_CACHE_NAME = "af1_xpehh_gwss_v1" -IHS_GWSS_CACHE_NAME = "af1_ihs_gwss_v1" +XPEHH_GWSS_CACHE_NAME = "af1_xpehh_gwss_v2" +IHS_GWSS_CACHE_NAME = "af1_ihs_gwss_v2" TAXON_PALETTE = px.colors.qualitative.Plotly TAXON_COLORS = { diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py index 38135389..9b29a3bd 100644 --- a/malariagen_data/ag3.py +++ b/malariagen_data/ag3.py @@ -17,8 +17,8 @@ GCS_REGION_URLS = { "us-central1": "gs://vo_agam_release_master_us_central1", } -XPEHH_GWSS_CACHE_NAME = "ag3_xpehh_gwss_v1" -IHS_GWSS_CACHE_NAME = "ag3_ihs_gwss_v1" +XPEHH_GWSS_CACHE_NAME = "ag3_xpehh_gwss_v2" +IHS_GWSS_CACHE_NAME = "ag3_ihs_gwss_v2" VIRTUAL_CONTIGS = { "2RL": ("2R", "2L"), "3RL": ("3R", "3L"), diff --git a/malariagen_data/anoph/fst.py b/malariagen_data/anoph/fst.py index ea096158..cae8a391 100644 --- a/malariagen_data/anoph/fst.py +++ b/malariagen_data/anoph/fst.py @@ -11,7 +11,7 @@ from .snp_data import AnophelesSnpData from . import base_params, fst_params, gplt_params, plotly_params -from ..util import CacheMiss, check_types +from ..util import CacheMiss, check_types, _resolve_region_with_deprec_contig_param class AnophelesFstAnalysis( @@ -29,7 +29,7 @@ def __init__( def _fst_gwss( self, *, - contig, + region, window_size, sample_sets, cohort1_query, @@ -46,7 +46,7 @@ def _fst_gwss( ): # Compute allele counts. ac1 = self.snp_allele_counts( - region=contig, + region=region, sample_query=cohort1_query, sample_query_options=sample_query_options, sample_sets=sample_sets, @@ -59,7 +59,7 @@ def _fst_gwss( chunks=chunks, ) ac2 = self.snp_allele_counts( - region=contig, + region=region, sample_query=cohort2_query, sample_query_options=sample_query_options, sample_sets=sample_sets, @@ -74,7 +74,7 @@ def _fst_gwss( with self._spinner(desc="Load SNP positions"): pos = self.snp_sites( - region=contig, + region=region, field="POS", site_mask=site_mask, inline_array=inline_array, @@ -105,10 +105,10 @@ def _fst_gwss( ) def fst_gwss( self, - contig: base_params.contig, - window_size: fst_params.window_size, - cohort1_query: base_params.sample_query, - cohort2_query: base_params.sample_query, + region: Optional[base_params.region] = None, + window_size: Optional[fst_params.window_size] = None, + cohort1_query: Optional[base_params.sample_query] = None, + cohort2_query: Optional[base_params.sample_query] = None, sample_query_options: Optional[base_params.sample_query_options] = None, sample_sets: Optional[base_params.sample_sets] = None, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, @@ -123,13 +123,37 @@ def fst_gwss( inline_array: base_params.inline_array = base_params.inline_array_default, chunks: base_params.chunks = base_params.native_chunks, clip_min: fst_params.clip_min = 0.0, + contig: Optional[base_params.region] = None, # Deprecated ) -> Tuple[np.ndarray, np.ndarray]: # Change this name if you ever change the behaviour of this function, to # invalidate any previously cached data. - name = "fst_gwss_v2" + name = "fst_gwss_v3" + + # Get a copy of the local variables, which will include all provided function parameters. + local_vars = locals().copy() + + # Specify which quasi-positional args are required. + # Note: to avoid this, we should move towards a keyword-only version of this function. + required_args = ("window_size", "cohort1_query", "cohort2_query") + + # Raise an error for any missing required args. + missing_args = [] + for required_arg in required_args: + if local_vars.get(required_arg) is None: + missing_args.append(required_arg) + if missing_args: + raise ValueError(f"Missing required arguments: {missing_args}") + + resolved_region = _resolve_region_with_deprec_contig_param( + region=region, contig=contig + ) + + # Delete original parameters to prevent accidental use. + del region + del contig params = dict( - contig=contig, + region=resolved_region, window_size=window_size, cohort1_query=cohort1_query, cohort2_query=cohort2_query, @@ -164,7 +188,7 @@ def fst_gwss( ) def plot_fst_gwss_track( self, - contig: base_params.contig, + region: base_params.region, window_size: fst_params.window_size, cohort1_query: base_params.sample_query, cohort2_query: base_params.sample_query, @@ -190,7 +214,7 @@ def plot_fst_gwss_track( ) -> gplt_params.optional_figure: # compute Fst x, fst = self.fst_gwss( - contig=contig, + region=region, window_size=window_size, cohort_size=cohort_size, min_cohort_size=min_cohort_size, @@ -253,7 +277,7 @@ def plot_fst_gwss_track( # tidy up the plot fig.yaxis.axis_label = "Fst" fig.yaxis.ticker = [0, 1] - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) @@ -270,7 +294,7 @@ def plot_fst_gwss_track( ) def plot_fst_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: fst_params.window_size, cohort1_query: base_params.sample_query, cohort2_query: base_params.sample_query, @@ -298,7 +322,7 @@ def plot_fst_gwss( ) -> gplt_params.optional_figure: # gwss track fig1 = self.plot_fst_gwss_track( - contig=contig, + region=region, window_size=window_size, cohort1_query=cohort1_query, cohort2_query=cohort2_query, @@ -322,7 +346,7 @@ def plot_fst_gwss( # plot genes fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, diff --git a/malariagen_data/anoph/g123.py b/malariagen_data/anoph/g123.py index dca996aa..e08d6262 100644 --- a/malariagen_data/anoph/g123.py +++ b/malariagen_data/anoph/g123.py @@ -37,7 +37,7 @@ def __init__( def _load_data_for_g123( self, *, - contig, + region, sites, site_mask, sample_sets, @@ -50,7 +50,7 @@ def _load_data_for_g123( chunks, ): ds_snps = self.snp_calls( - region=contig, + region=region, sample_query=sample_query, sample_query_options=sample_query_options, sample_sets=sample_sets, @@ -74,7 +74,7 @@ def _load_data_for_g123( # of samples was used to set up the phasing analysis. with self._spinner("Subsetting to selected sites"): haplotype_pos = self.haplotype_sites( - region=contig, + region=region, analysis=sites, field="POS", inline_array=True, @@ -106,7 +106,7 @@ def _load_data_for_g123( def _g123_gwss( self, *, - contig, + region, sites, site_mask, window_size, @@ -120,7 +120,7 @@ def _g123_gwss( chunks, ): gt, pos = self._load_data_for_g123( - contig=contig, + region=region, sites=sites, site_mask=site_mask, sample_sets=sample_sets, @@ -151,7 +151,7 @@ def _g123_gwss( ) def g123_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: g123_params.window_size, sites: g123_params.sites = base_params.DEFAULT, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, @@ -170,7 +170,7 @@ def g123_gwss( ) -> Tuple[np.ndarray, np.ndarray]: # Change this name if you ever change the behaviour of this function, to # invalidate any previously cached data. - name = "g123_gwss_v1" + name = "g123_gwss_v2" if sites == base_params.DEFAULT: assert self._default_phasing_analysis is not None @@ -182,7 +182,7 @@ def g123_gwss( ) params = dict( - contig=contig, + region=region, sites=sites, site_mask=site_mask, window_size=window_size, @@ -214,7 +214,7 @@ def g123_gwss( def _g123_calibration( self, *, - contig, + region, sites, site_mask, sample_query, @@ -228,7 +228,7 @@ def _g123_calibration( chunks, ) -> Mapping[str, np.ndarray]: gt, _ = self._load_data_for_g123( - contig=contig, + region=region, sites=sites, site_mask=site_mask, sample_query=sample_query, @@ -258,7 +258,7 @@ def _g123_calibration( ) def g123_calibration( self, - contig: base_params.contig, + region: base_params.region, sites: g123_params.sites = base_params.DEFAULT, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, sample_query: Optional[base_params.sample_query] = None, @@ -280,7 +280,7 @@ def g123_calibration( name = "g123_calibration_v1" params = dict( - contig=contig, + region=region, sites=sites, site_mask=self._prep_optional_site_mask_param(site_mask=site_mask), window_sizes=window_sizes, @@ -312,7 +312,7 @@ def g123_calibration( ) def plot_g123_gwss_track( self, - contig: base_params.contig, + region: base_params.region, window_size: g123_params.window_size, sites: g123_params.sites = base_params.DEFAULT, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, @@ -338,7 +338,7 @@ def plot_g123_gwss_track( ) -> gplt_params.optional_figure: # compute G123 x, g123 = self.g123_gwss( - contig=contig, + region=region, sites=sites, site_mask=site_mask, window_size=window_size, @@ -401,7 +401,7 @@ def plot_g123_gwss_track( # tidy up the plot fig.yaxis.axis_label = "G123" fig.yaxis.ticker = [0, 1] - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) @@ -415,7 +415,7 @@ def plot_g123_gwss_track( ) def plot_g123_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: g123_params.window_size, sites: g123_params.sites = base_params.DEFAULT, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, @@ -443,7 +443,7 @@ def plot_g123_gwss( ) -> gplt_params.optional_figure: # gwss track fig1 = self.plot_g123_gwss_track( - contig=contig, + region=region, sites=sites, site_mask=site_mask, window_size=window_size, @@ -467,7 +467,7 @@ def plot_g123_gwss( # plot genes fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, @@ -500,7 +500,7 @@ def plot_g123_gwss( ) def plot_g123_calibration( self, - contig: base_params.contig, + region: base_params.region, sites: g123_params.sites, site_mask: Optional[base_params.site_mask] = base_params.DEFAULT, sample_query: Optional[base_params.sample_query] = None, @@ -521,7 +521,7 @@ def plot_g123_calibration( ) -> gplt_params.optional_figure: # get g123 values calibration_runs = self.g123_calibration( - contig=contig, + region=region, sites=sites, site_mask=site_mask, sample_query=sample_query, diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py index 3e211eeb..c3dc09f7 100644 --- a/malariagen_data/anoph/h12.py +++ b/malariagen_data/anoph/h12.py @@ -25,7 +25,7 @@ def __init__( def _h12_calibration( self, - contig, + region, analysis, sample_query, sample_query_options, @@ -39,7 +39,7 @@ def _h12_calibration( inline_array, ) -> Mapping[str, np.ndarray]: ds_haps = self.haplotypes( - region=contig, + region=region, sample_sets=sample_sets, sample_query=sample_query, sample_query_options=sample_query_options, @@ -73,7 +73,7 @@ def _h12_calibration( ) def h12_calibration( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_query: Optional[base_params.sample_query] = None, sample_query_options: Optional[base_params.sample_query_options] = None, @@ -95,7 +95,7 @@ def h12_calibration( name = "h12_calibration_v1" params = dict( - contig=contig, + region=region, analysis=self._prep_phasing_analysis_param(analysis=analysis), window_sizes=window_sizes, sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets), @@ -131,7 +131,7 @@ def h12_calibration( ) def plot_h12_calibration( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_query: Optional[base_params.sample_query] = None, sample_query_options: Optional[base_params.sample_query_options] = None, @@ -152,7 +152,7 @@ def plot_h12_calibration( ) -> gplt_params.optional_figure: # Get H12 values. calibration_runs = self.h12_calibration( - contig=contig, + region=region, analysis=analysis, sample_query=sample_query, sample_query_options=sample_query_options, @@ -227,7 +227,7 @@ def plot_h12_calibration( def _h12_gwss( self, - contig, + region, analysis, window_size, sample_sets, @@ -241,7 +241,7 @@ def _h12_gwss( inline_array, ): ds_haps = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=sample_query, sample_query_options=sample_query_options, @@ -289,7 +289,7 @@ def _h12_gwss( ) def h12_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, analysis: hap_params.analysis = base_params.DEFAULT, sample_query: Optional[base_params.sample_query] = None, @@ -308,10 +308,10 @@ def h12_gwss( ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: # Change this name if you ever change the behaviour of this function, to # invalidate any previously cached data. - name = "h12_gwss_v2" + name = "h12_gwss_v3" params = dict( - contig=contig, + region=region, analysis=self._prep_phasing_analysis_param(analysis=analysis), window_size=window_size, sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets), @@ -345,7 +345,7 @@ def h12_gwss( ) def plot_h12_gwss_track( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, @@ -372,7 +372,7 @@ def plot_h12_gwss_track( ) -> gplt_params.optional_figure: # Compute H12. x, h12, contigs = self.h12_gwss( - contig=contig, + region=region, analysis=analysis, window_size=window_size, cohort_size=cohort_size, @@ -434,7 +434,7 @@ def plot_h12_gwss_track( # Tidy up the plot. fig.yaxis.axis_label = "H12" fig.yaxis.ticker = [0, 1] - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) @@ -448,7 +448,7 @@ def plot_h12_gwss_track( ) def plot_h12_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, @@ -477,7 +477,7 @@ def plot_h12_gwss( ) -> gplt_params.optional_figure: # Plot GWSS track. fig1 = self.plot_h12_gwss_track( - contig=contig, + region=region, analysis=analysis, window_size=window_size, sample_sets=sample_sets, @@ -502,7 +502,7 @@ def plot_h12_gwss( # Plot genes. fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, @@ -535,7 +535,7 @@ def plot_h12_gwss( ) def plot_h12_gwss_multi_overlay_track( self, - contig: base_params.contig, + region: base_params.region, cohorts: base_params.cohorts, window_size: h12_params.multi_window_size, cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default, @@ -578,7 +578,7 @@ def plot_h12_gwss_multi_overlay_track( res = {} for cohort_label, cohort_query in cohort_queries.items(): res[cohort_label] = self.h12_gwss( - contig=contig, + region=region, analysis=analysis, window_size=window_size[cohort_label], cohort_size=cohort_size, @@ -654,7 +654,7 @@ def plot_h12_gwss_multi_overlay_track( ) def plot_h12_gwss_multi_overlay( self, - contig: base_params.contig, + region: base_params.region, cohorts: base_params.cohorts, window_size: h12_params.multi_window_size, cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default, @@ -682,7 +682,7 @@ def plot_h12_gwss_multi_overlay( ) -> gplt_params.optional_figure: # Plot GWSS track. fig1 = self.plot_h12_gwss_multi_overlay_track( - contig=contig, + region=region, sample_query=sample_query, cohorts=cohorts, cohort_size=cohort_size, @@ -708,7 +708,7 @@ def plot_h12_gwss_multi_overlay( # Plot genes. fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, @@ -741,7 +741,7 @@ def plot_h12_gwss_multi_overlay( ) def plot_h12_gwss_multi_panel( self, - contig: base_params.contig, + region: base_params.region, cohorts: base_params.cohorts, window_size: h12_params.multi_window_size, cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default, @@ -784,7 +784,7 @@ def plot_h12_gwss_multi_panel( figs: list[gplt_params.figure] = [] for i, (cohort_label, cohort_query) in enumerate(cohort_queries.items()): params = dict( - contig=contig, + region=region, analysis=analysis, window_size=window_size[cohort_label], sample_sets=sample_sets, @@ -809,7 +809,7 @@ def plot_h12_gwss_multi_panel( # Plot genes. fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py index 79e5b1ab..1f092764 100644 --- a/malariagen_data/anoph/h1x.py +++ b/malariagen_data/anoph/h1x.py @@ -26,7 +26,7 @@ def __init__( def _h1x_gwss( self, *, - contig, + region, analysis, window_size, sample_sets, @@ -42,7 +42,7 @@ def _h1x_gwss( ): # Access haplotype datasets for each cohort. ds1 = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=cohort1_query, sample_query_options=sample_query_options, @@ -55,7 +55,7 @@ def _h1x_gwss( inline_array=inline_array, ) ds2 = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=cohort2_query, sample_query_options=sample_query_options, @@ -110,7 +110,7 @@ def _h1x_gwss( ) def h1x_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, cohort1_query: base_params.sample_query, cohort2_query: base_params.sample_query, @@ -130,10 +130,10 @@ def h1x_gwss( ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: # Change this name if you ever change the behaviour of this function, to # invalidate any previously cached data. - name = "h1x_gwss_v2" + name = "h1x_gwss_v3" params = dict( - contig=contig, + region=region, analysis=self._prep_phasing_analysis_param(analysis=analysis), window_size=window_size, # N.B., do not be tempted to convert these sample queries into integer @@ -171,7 +171,7 @@ def h1x_gwss( ) def plot_h1x_gwss_track( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, cohort1_query: base_params.cohort1_query, cohort2_query: base_params.cohort2_query, @@ -199,7 +199,7 @@ def plot_h1x_gwss_track( ) -> gplt_params.optional_figure: # Compute H1X. x, h1x, contigs = self.h1x_gwss( - contig=contig, + region=region, analysis=analysis, window_size=window_size, cohort_size=cohort_size, @@ -262,7 +262,7 @@ def plot_h1x_gwss_track( # Tidy up the plot. fig.yaxis.axis_label = "H1X" fig.yaxis.ticker = [0, 1] - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) @@ -279,7 +279,7 @@ def plot_h1x_gwss_track( ) def plot_h1x_gwss( self, - contig: base_params.contig, + region: base_params.region, window_size: h12_params.window_size, cohort1_query: base_params.cohort1_query, cohort2_query: base_params.cohort2_query, @@ -309,7 +309,7 @@ def plot_h1x_gwss( ) -> gplt_params.optional_figure: # Plot GWSS track. fig1 = self.plot_h1x_gwss_track( - contig=contig, + region=region, analysis=analysis, window_size=window_size, cohort1_query=cohort1_query, @@ -335,7 +335,7 @@ def plot_h1x_gwss( # Plot genes. fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py index d6b58066..03e1f15a 100644 --- a/malariagen_data/anopheles.py +++ b/malariagen_data/anopheles.py @@ -1278,7 +1278,7 @@ def plot_diversity_stats( ) def ihs_gwss( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, sample_query: Optional[base_params.sample_query] = None, @@ -1311,7 +1311,7 @@ def ihs_gwss( name = self._ihs_gwss_cache_name params = dict( - contig=contig, + region=region, analysis=self._prep_phasing_analysis_param(analysis=analysis), window_size=window_size, percentiles=percentiles, @@ -1352,7 +1352,7 @@ def ihs_gwss( def _ihs_gwss( self, *, - contig, + region, analysis, sample_sets, sample_query, @@ -1377,7 +1377,7 @@ def _ihs_gwss( inline_array, ): ds_haps = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=sample_query, sample_query_options=sample_query_options, @@ -1451,7 +1451,7 @@ def _ihs_gwss( ) def plot_ihs_gwss_track( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, sample_query: Optional[base_params.sample_query] = None, @@ -1489,7 +1489,7 @@ def plot_ihs_gwss_track( ) -> gplt_params.optional_figure: # compute ihs x, ihs = self.ihs_gwss( - contig=contig, + region=region, analysis=analysis, window_size=window_size, percentiles=percentiles, @@ -1583,7 +1583,7 @@ def plot_ihs_gwss_track( # tidy up the plot fig.yaxis.axis_label = "ihs" - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) @@ -1597,7 +1597,7 @@ def plot_ihs_gwss_track( ) def plot_xpehh_gwss( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, cohort1_query: Optional[base_params.sample_query] = None, @@ -1634,7 +1634,7 @@ def plot_xpehh_gwss( ) -> gplt_params.optional_figure: # gwss track fig1 = self.plot_xpehh_gwss_track( - contig=contig, + region=region, analysis=analysis, sample_sets=sample_sets, cohort1_query=cohort1_query, @@ -1668,7 +1668,7 @@ def plot_xpehh_gwss( # plot genes fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, @@ -1699,7 +1699,7 @@ def plot_xpehh_gwss( ) def plot_ihs_gwss( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, sample_query: Optional[base_params.sample_query] = None, @@ -1739,7 +1739,7 @@ def plot_ihs_gwss( ) -> gplt_params.optional_figure: # gwss track fig1 = self.plot_ihs_gwss_track( - contig=contig, + region=region, analysis=analysis, sample_sets=sample_sets, sample_query=sample_query, @@ -1775,7 +1775,7 @@ def plot_ihs_gwss( # plot genes fig2 = self.plot_genes( - region=contig, + region=region, sizing_mode=sizing_mode, width=width, height=genes_height, @@ -1811,7 +1811,7 @@ def plot_ihs_gwss( ) def xpehh_gwss( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, cohort1_query: Optional[base_params.sample_query] = None, @@ -1841,7 +1841,7 @@ def xpehh_gwss( name = self._xpehh_gwss_cache_name params = dict( - contig=contig, + region=region, analysis=self._prep_phasing_analysis_param(analysis=analysis), window_size=window_size, percentiles=percentiles, @@ -1881,7 +1881,7 @@ def xpehh_gwss( def _xpehh_gwss( self, *, - contig, + region, analysis, sample_sets, cohort1_query, @@ -1903,7 +1903,7 @@ def _xpehh_gwss( inline_array, ): ds_haps1 = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=cohort1_query, sample_query_options=sample_query_options, @@ -1916,7 +1916,7 @@ def _xpehh_gwss( ) ds_haps2 = self.haplotypes( - region=contig, + region=region, analysis=analysis, sample_query=cohort2_query, sample_query_options=sample_query_options, @@ -1987,7 +1987,7 @@ def _xpehh_gwss( ) def plot_xpehh_gwss_track( self, - contig: base_params.contig, + region: base_params.region, analysis: hap_params.analysis = base_params.DEFAULT, sample_sets: Optional[base_params.sample_sets] = None, cohort1_query: Optional[base_params.sample_query] = None, @@ -2022,7 +2022,7 @@ def plot_xpehh_gwss_track( ) -> gplt_params.optional_figure: # compute xpehh x, xpehh = self.xpehh_gwss( - contig=contig, + region=region, analysis=analysis, window_size=window_size, percentiles=percentiles, @@ -2115,7 +2115,7 @@ def plot_xpehh_gwss_track( # tidy up the plot fig.yaxis.axis_label = "XP-EHH" - self._bokeh_style_genome_xaxis(fig, contig) + self._bokeh_style_genome_xaxis(fig, region) if show: # pragma: no cover bokeh.plotting.show(fig) diff --git a/malariagen_data/util.py b/malariagen_data/util.py index bb4b7e9e..08f0878b 100644 --- a/malariagen_data/util.py +++ b/malariagen_data/util.py @@ -1603,3 +1603,30 @@ def add_frequency_ci(*, ds, ci_method): ) ds["event_frequency_ci_low"] = ("variants", "cohorts"), frq_ci_low ds["event_frequency_ci_upp"] = ("variants", "cohorts"), frq_ci_upp + + +def _resolve_region_with_deprec_contig_param(*, region, contig): + """ + This helper function should be used by any public function that accepts both a `region` and a `contig` parameter. + The `contig` parameter is now deprecated, so we need to determine which value the `region` should have. + This function returns the determined value for the `region` based on the given parameters. + """ + + if contig is None: + # A `contig` has not been given, so return whatever `region` is. + return region + elif region is None: + # A `contig` has been given, and a `region` has not been given. + # Raise a `DeprecationWarning` for the `contig` param. + # Note: this might not be shown due to warning filters. + warnings.warn( + "The 'contig' parameter has been deprecated. Please use 'region' instead.", + DeprecationWarning, + ) + # The given `contig` should be a valid `region`, so return the given `contig` as the region. + return contig + else: + # Both a `contig` and a `region` have been given. + raise ValueError( + "Both 'region' and 'contig' parameters were provided. Please provide a 'region' parameter only. The 'contig' parameter has been deprecated." + ) diff --git a/notebooks/plot_fst_gwss.ipynb b/notebooks/plot_fst_gwss.ipynb index a627356d..46274629 100644 --- a/notebooks/plot_fst_gwss.ipynb +++ b/notebooks/plot_fst_gwss.ipynb @@ -54,7 +54,7 @@ "outputs": [], "source": [ "ag3.plot_fst_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=10_000,\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " cohort2_query=\"cohort_admin2_year == 'ML-2_Kati_gamb_2014'\",\n", @@ -72,7 +72,7 @@ "outputs": [], "source": [ "ag3.plot_fst_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=10_000,\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " cohort2_query=\"cohort_admin2_year == 'ML-2_Kati_gamb_2014'\",\n", @@ -92,7 +92,7 @@ "outputs": [], "source": [ "ag3.plot_fst_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=10_000,\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " cohort2_query=\"cohort_admin2_year == 'ML-2_Kati_gamb_2014'\",\n", @@ -110,7 +110,7 @@ "outputs": [], "source": [ "ag3.plot_fst_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=10_000,\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " cohort2_query=\"country == 'Mayotte' and taxon == 'gambiae'\",\n", @@ -128,7 +128,7 @@ "outputs": [], "source": [ "af1.plot_fst_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=20_000,\n", " cohort1_query=\"cohort_admin1_year == 'KE-03_fune_2016'\",\n", " cohort2_query=\"cohort_admin1_year == 'MZ-L_fune_2016'\",\n", @@ -145,7 +145,7 @@ "outputs": [], "source": [ "af1.plot_fst_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=20_000,\n", " cohort1_query=\"cohort_admin1_year == 'KE-03_fune_2016'\",\n", " cohort2_query=\"cohort_admin1_year == 'MZ-L_fune_2016'\",\n", @@ -173,7 +173,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "mgen_data_py3.11", "language": "python", "name": "python3" }, @@ -187,7 +187,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/plot_g123_gwss.ipynb b/notebooks/plot_g123_gwss.ipynb index 73ac584a..396b241d 100644 --- a/notebooks/plot_g123_gwss.ipynb +++ b/notebooks/plot_g123_gwss.ipynb @@ -68,7 +68,7 @@ "source": [ "%%time\n", "ag3.plot_g123_calibration(\n", - " contig=contig,\n", + " region=contig,\n", " sites=site_mask,\n", " sample_sets=sample_set,\n", " sample_query=sample_query,\n", @@ -85,7 +85,7 @@ "source": [ "%%time\n", "ag3.plot_g123_calibration(\n", - " contig=contig,\n", + " region=contig,\n", " sites=site_mask,\n", " sample_sets=sample_set,\n", " sample_query=sample_query,\n", @@ -102,7 +102,7 @@ "source": [ "%%time\n", "ag3.plot_g123_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " site_mask=site_mask,\n", " sites=site_mask,\n", @@ -121,7 +121,7 @@ "source": [ "%%time\n", "ag3.plot_g123_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " site_mask=site_mask,\n", " sites=site_mask,\n", @@ -140,7 +140,7 @@ "source": [ "%%time\n", "ag3.plot_g123_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " site_mask=site_mask,\n", " sites=\"segregating\",\n", @@ -161,7 +161,7 @@ "source": [ "%%time\n", "ag3.plot_g123_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " site_mask=site_mask,\n", " sites=\"all\",\n", @@ -181,7 +181,7 @@ "source": [ "%%time\n", "ag3.plot_g123_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " site_mask=site_mask,\n", " sites=site_mask,\n", @@ -219,7 +219,7 @@ "outputs": [], "source": [ "af1.plot_g123_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=2_000,\n", " sites=\"segregating\",\n", " site_mask=\"funestus\",\n", @@ -237,7 +237,7 @@ "outputs": [], "source": [ "af1.plot_g123_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=2000,\n", " site_mask=\"funestus\",\n", " sites=\"funestus\",\n", @@ -258,7 +258,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "mgen_data_py3.11", "language": "python", "name": "python3" }, @@ -272,7 +272,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/plot_h12_h1x.ipynb b/notebooks/plot_h12_h1x.ipynb index 33e00f53..7adf51f3 100644 --- a/notebooks/plot_h12_h1x.ipynb +++ b/notebooks/plot_h12_h1x.ipynb @@ -89,7 +89,7 @@ "outputs": [], "source": [ "ag3.plot_h12_calibration(\n", - " contig=contig,\n", + " region=contig,\n", " analysis=\"gamb_colu\",\n", " sample_query=coh1_query,\n", " sample_sets=\"3.0\",\n", @@ -106,7 +106,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " analysis=\"gamb_colu\",\n", " window_size=2000,\n", " sample_query=coh1_query,\n", @@ -123,7 +123,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss(\n", - " contig=contigs,\n", + " region=contigs,\n", " analysis=\"gamb_colu\",\n", " window_size=2000,\n", " sample_query=coh1_query,\n", @@ -142,7 +142,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " analysis=\"gamb_colu\",\n", " window_size=2000,\n", " sample_query=coh1_query,\n", @@ -162,7 +162,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " analysis=\"gamb_colu\",\n", " window_size=2000,\n", " sample_query=coh2_query,\n", @@ -181,7 +181,7 @@ "outputs": [], "source": [ "ag3.plot_h1x_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " cohort1_query=coh1_query,\n", " cohort2_query=coh2_query,\n", @@ -199,7 +199,7 @@ "outputs": [], "source": [ "ag3.plot_h1x_gwss(\n", - " contig=contigs,\n", + " region=contigs,\n", " window_size=2000,\n", " cohort1_query=coh1_query,\n", " cohort2_query=coh2_query,\n", @@ -232,7 +232,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss_multi_overlay(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " cohorts=\"admin2_year\",\n", " sample_sets=\"AG1000G-ML-A\",\n", @@ -251,7 +251,7 @@ "outputs": [], "source": [ "ag3.plot_h12_gwss_multi_panel(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " cohorts=\"admin2_year\",\n", " sample_sets=\"AG1000G-ML-A\",\n", @@ -322,7 +322,7 @@ "outputs": [], "source": [ "af1.plot_h12_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " sample_query=coh1_query,\n", " sample_sets=\"1.0\",\n", @@ -338,7 +338,7 @@ "outputs": [], "source": [ "af1.plot_h12_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " sample_query=coh2_query,\n", " sample_sets=\"1.0\",\n", @@ -375,7 +375,7 @@ "outputs": [], "source": [ "af1.plot_h12_gwss_multi_overlay(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=window_size,\n", " cohorts=cohorts,\n", " sample_sets=\"1.0\",\n", @@ -393,7 +393,7 @@ "outputs": [], "source": [ "af1.plot_h12_gwss_multi_panel(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=window_size,\n", " cohorts=cohorts,\n", " sample_sets=\"1.0\",\n", @@ -409,7 +409,7 @@ "outputs": [], "source": [ "af1.plot_h1x_gwss(\n", - " contig=contig,\n", + " region=contig,\n", " window_size=2000,\n", " cohort1_query=coh1_query,\n", " cohort2_query=coh2_query,\n", @@ -427,7 +427,7 @@ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m125" }, "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "mgen_data_py3.11", "language": "python", "name": "python3" }, @@ -441,12 +441,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.11" - }, - "vscode": { - "interpreter": { - "hash": "3b9ddb1005cd06989fd869b9e3d566470f1be01faa610bb17d64e58e32302e8b" - } + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/plot_ihs_gwss.ipynb b/notebooks/plot_ihs_gwss.ipynb index 4a8fa53c..d08ed48d 100644 --- a/notebooks/plot_ihs_gwss.ipynb +++ b/notebooks/plot_ihs_gwss.ipynb @@ -42,7 +42,7 @@ "outputs": [], "source": [ "ag3.plot_ihs_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " analysis=\"gamb_colu\",\n", " percentiles=(50, 60, 90, 100),\n", @@ -60,7 +60,7 @@ "outputs": [], "source": [ "ag3.plot_ihs_gwss_track(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1000,\n", " analysis=\"gamb_colu\",\n", " sample_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", @@ -81,7 +81,7 @@ "outputs": [], "source": [ "ag3.plot_ihs_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=100,\n", " sample_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " sample_sets=\"3.0\",\n", @@ -99,7 +99,7 @@ "outputs": [], "source": [ "ag3.plot_ihs_gwss(\n", - " contig=\"2L\",\n", + " region=\"2L\",\n", " window_size=1_000,\n", " sample_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", " sample_sets=\"3.0\",\n", @@ -127,7 +127,7 @@ "outputs": [], "source": [ "af1.plot_ihs_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=2_000,\n", " sample_query=\"cohort_admin1_year == 'KE-03_fune_2016'\",\n", " sample_sets=\"1.0\",\n", @@ -143,7 +143,7 @@ "outputs": [], "source": [ "af1.plot_ihs_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=200,\n", " sample_query=\"cohort_admin1_year == 'KE-03_fune_2016'\",\n", " sample_sets=\"1.0\",\n", @@ -162,7 +162,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "mgen_data_py3.11", "language": "python", "name": "python3" }, @@ -176,7 +176,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/plot_xpehh_gwss.ipynb b/notebooks/plot_xpehh_gwss.ipynb index cd9e6758..2155ea07 100644 --- a/notebooks/plot_xpehh_gwss.ipynb +++ b/notebooks/plot_xpehh_gwss.ipynb @@ -40,7 +40,7 @@ "outputs": [], "source": [ "ag3.plot_xpehh_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=1_000,\n", " analysis=\"gamb_colu\",\n", " percentiles=(50, 60, 90, 100),\n", @@ -59,7 +59,7 @@ "outputs": [], "source": [ "ag3.plot_xpehh_gwss_track(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=1_000,\n", " analysis=\"gamb_colu\",\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", @@ -80,7 +80,7 @@ "outputs": [], "source": [ "ag3.plot_xpehh_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=100,\n", " analysis=\"gamb_colu\",\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", @@ -98,7 +98,7 @@ "outputs": [], "source": [ "ag3.plot_xpehh_gwss(\n", - " contig=\"2RL\",\n", + " region=\"2RL\",\n", " window_size=100,\n", " analysis=\"gamb_colu\",\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", @@ -116,7 +116,7 @@ "outputs": [], "source": [ "ag3.plot_xpehh_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=1_000,\n", " analysis=\"gamb_colu\",\n", " cohort1_query=\"cohort_admin2_year == 'ML-2_Kati_colu_2014'\",\n", @@ -145,7 +145,7 @@ "outputs": [], "source": [ "af1.plot_xpehh_gwss(\n", - " contig=\"X\",\n", + " region=\"X\",\n", " window_size=2_000,\n", " cohort1_query=\"cohort_admin1_year == 'MZ-L_fune_2018'\",\n", " cohort2_query=\"cohort_admin1_year == 'GA-2_fune_2017'\",\n", @@ -162,7 +162,7 @@ "outputs": [], "source": [ "af1.plot_xpehh_gwss(\n", - " contig=\"2RL\",\n", + " region=\"2RL\",\n", " window_size=200,\n", " cohort1_query=\"cohort_admin1_year == 'MZ-L_fune_2018'\",\n", " cohort2_query=\"cohort_admin1_year == 'GA-2_fune_2017'\",\n", @@ -182,7 +182,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "mgen_data_py3.11", "language": "python", "name": "python3" }, @@ -196,7 +196,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.5" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py index 098f0853..712cc7e1 100644 --- a/tests/anoph/test_fst.py +++ b/tests/anoph/test_fst.py @@ -86,7 +86,7 @@ def test_fst_gwss(fixture, api: AnophelesFstAnalysis): cohort1_query = f"country == {countries[0]!r}" cohort2_query = f"country == {countries[1]!r}" fst_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=all_sample_sets, cohort1_query=cohort1_query, cohort2_query=cohort2_query, diff --git a/tests/anoph/test_g123.py b/tests/anoph/test_g123.py index ab5e2553..db2d0611 100644 --- a/tests/anoph/test_g123.py +++ b/tests/anoph/test_g123.py @@ -103,7 +103,7 @@ def test_g123_gwss_with_default_sites(fixture, api: AnophelesG123Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=10_000), sample_sets=[random.choice(all_sample_sets)], window_size=random.randint(100, 500), min_cohort_size=10, @@ -118,7 +118,7 @@ def test_g123_gwss_with_phased_sites(fixture, api: AnophelesG123Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=10_000), sites=random.choice(api.phasing_analysis_ids), sample_sets=[random.choice(all_sample_sets)], window_size=random.randint(100, 500), @@ -134,7 +134,7 @@ def test_g123_gwss_with_segregating_sites(fixture, api: AnophelesG123Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sites="segregating", site_mask=random.choice(api.site_mask_ids), sample_sets=[random.choice(all_sample_sets)], @@ -151,7 +151,7 @@ def test_g123_gwss_with_all_sites(fixture, api: AnophelesG123Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sites="all", site_mask=None, sample_sets=[random.choice(all_sample_sets)], @@ -168,7 +168,7 @@ def test_g123_gwss_with_bad_sites(fixture, api: AnophelesG123Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=[random.choice(all_sample_sets)], window_size=random.randint(100, 500), min_cohort_size=10, @@ -187,7 +187,7 @@ def test_g123_calibration(fixture, api: AnophelesG123Analysis): window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist() window_sizes = sorted([int(x) for x in window_sizes]) g123_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=10_000), sites=random.choice(api.phasing_analysis_ids), sample_sets=[random.choice(all_sample_sets)], min_cohort_size=10, diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py index 29262e94..7c852151 100644 --- a/tests/anoph/test_h12.py +++ b/tests/anoph/test_h12.py @@ -107,7 +107,7 @@ def test_h12_calibration(fixture, api: AnophelesH12Analysis): window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist() window_sizes = sorted(set([int(x) for x in window_sizes])) h12_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=[random.choice(all_sample_sets)], window_sizes=window_sizes, min_cohort_size=5, @@ -170,7 +170,7 @@ def test_h12_gwss_with_default_analysis(fixture, api: AnophelesH12Analysis): # Set up test parameters. all_sample_sets = api.sample_sets()["sample_set"].to_list() h12_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=[random.choice(all_sample_sets)], window_size=random.randint(100, 500), min_cohort_size=5, @@ -199,7 +199,7 @@ def test_h12_gwss_with_analysis(fixture, api: AnophelesH12Analysis): # No samples available, check similar error raised from H12. with pytest.raises(ValueError): api.h12_gwss( - contig=contig, + region=contig, sample_sets=sample_sets, analysis=analysis, window_size=window_size, @@ -210,7 +210,7 @@ def test_h12_gwss_with_analysis(fixture, api: AnophelesH12Analysis): # Samples are available, run full checks. n_samples = ds_hap.sizes["samples"] h12_params = dict( - contig=contig, + region=contig, sample_sets=sample_sets, analysis=analysis, window_size=window_size, @@ -221,7 +221,7 @@ def test_h12_gwss_with_analysis(fixture, api: AnophelesH12Analysis): # Check min_cohort_size behaviour. with pytest.raises(ValueError): api.h12_gwss( - contig=contig, + region=contig, sample_sets=sample_sets, analysis=analysis, window_size=window_size, @@ -238,7 +238,7 @@ def test_h12_gwss_multi_with_default_analysis(fixture, api: AnophelesH12Analysis cohort1_query = f"country == '{country1}'" cohort2_query = f"country == '{country2}'" h12_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=10_000), sample_sets=all_sample_sets, window_size=random.randint(100, 500), min_cohort_size=1, @@ -258,7 +258,7 @@ def test_h12_gwss_multi_with_window_size_dict(fixture, api: AnophelesH12Analysis cohort1_query = f"country == '{country1}'" cohort2_query = f"country == '{country2}'" h12_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=all_sample_sets, window_size={ "cohort1": random.randint(100, 500), @@ -311,7 +311,7 @@ def test_h12_gwss_multi_with_analysis(fixture, api: AnophelesH12Analysis): # Samples are available, run full checks. h12_params = dict( analysis=analysis, - contig=contig, + region=contig, sample_sets=all_sample_sets, window_size=random.randint(100, 500), min_cohort_size=min(n1, n2), diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py index 627717b5..4539a673 100644 --- a/tests/anoph/test_h1x.py +++ b/tests/anoph/test_h1x.py @@ -145,7 +145,7 @@ def test_h1x_gwss_with_default_analysis(fixture, api: AnophelesH1XAnalysis): cohort1_query = f"country == '{country1}'" cohort2_query = f"country == '{country2}'" h1x_params = dict( - contig=random.choice(api.contigs), + region=fixture.random_region_str(region_size=5000), sample_sets=all_sample_sets, window_size=random.randint(100, 500), min_cohort_size=1, @@ -196,7 +196,7 @@ def test_h1x_gwss_with_analysis(fixture, api: AnophelesH1XAnalysis): # Samples are available, run full checks. h1x_params = dict( analysis=analysis, - contig=contig, + region=contig, sample_sets=all_sample_sets, window_size=random.randint(100, 500), min_cohort_size=min(n1, n2), diff --git a/tests/integration/test_ag3.py b/tests/integration/test_ag3.py index c786c132..2070f4b3 100644 --- a/tests/integration/test_ag3.py +++ b/tests/integration/test_ag3.py @@ -104,13 +104,13 @@ def test_locate_region(region_raw): def test_ihs_gwss(): ag3 = setup_ag3(cohorts_analysis="20230516") sample_query = "country == 'Ghana'" - contig = "3L" + region = "3L" analysis = "gamb_colu" sample_sets = "3.0" window_size = 1000 x, ihs = ag3.ihs_gwss( - contig=contig, + region=region, analysis=analysis, sample_query=sample_query, sample_sets=sample_sets, @@ -140,7 +140,7 @@ def test_xpehh_gwss(): window_size = 1000 x, xpehh = ag3.xpehh_gwss( - contig=contig, + region=contig, analysis=analysis, cohort1_query=cohort1_query, cohort2_query=cohort2_query,