TODO (minor fixes)

[xin-huang]

Add temp() on

selscape/workflow/rules/5.2_balancing_selection_scikit-allel.smk

Line 43 in e5d6bac

formatted="results/balancing_selection/scikit-allel/{species}/{method}/{ppl}/{window}_{step}/chr{i}.{method}.tajima_d.formatted.txt",

[xin-huang]

add temp() in preprocess.smk and polarization.smk

[xin-huang]

Add temp() on

selscape/workflow/rules/5.2_balancing_selection_scikit-allel.smk

Line 43 in e5d6bac
formatted="results/balancing_selection/scikit-allel/{species}/{method}/{ppl}/{window}_{step}/chr{i}.{method}.tajima_d.formatted.txt",

completed in #7

[xin-huang]

I don't know whether this

selscape/workflow/rules/4.1_positive_selection_selscan.smk

Lines 261 to 263 in 3e965b0

	labels=lambda wildcards: selscan_labels(
	wildcards, type="Enrichment Table"
	),

can be replaced with

labels=selscan_labels( 
     type="Enrichment Table" 
 ), 

[xin-huang]

or maybe this

def selscan_xp_labels(type: str = "Manhattan Plot"):
    def _labels(wildcards) -> dict[str, str]:
        return {
            "Populations": _vs_pair(wildcards),
            "Minor Allele Frequency": wildcards.maf,
            "Threshold": _top_pct(wildcards),
            "Type": type,
        }
    return _labels

[xin-huang]

how to simply those lambda functions for adding titles, such as

selscape/workflow/rules/5.2_balancing_selection_scikit-allel.smk

Lines 254 to 255 in 3e965b0

	params:
	title=lambda w: f"{w.ppl} {w.method.upper().replace('_', ' ')} (Window={w.window}{' SNPs' if w.method == 'moving_tajima_d' else ' bp'}, Step={int(float(w.step) * int(w.window))}{' SNPs' if w.method == 'moving_tajima_d' else ' bp'}, Top {float(w.cutoff)*100:.2f}%) ENRICHMENT",

[xin-huang]

Estimated 95% uncertainties, not CI

selscape/workflow/rules/6_deleterious_dfe_dadi.smk

Line 363 in 3e965b0

title=lambda w: f"{w.ppl} {w.dfe.upper().replace('_', ' ')} DFE ({w.demog.upper().replace('_', ' ')}) GODAMBE 95% CI ({dadi_config['bootstrap_replicates']} bootstrap replicates, chunk size={dadi_config['chunk_size']} bp)"

[xin-huang]

chr

selscape/workflow/rules/4.1_positive_selection_selscan.smk

Line 230 in a9629ca

sed '1d' {input.candidates} | awk '{{print "chr"$1"\\t"$2}}' > {output.candidate_snps} 2> {log}

[xin-huang]

1pop

selscape/workflow/rules/5.2_balancing_selection_scikit-allel.smk

Lines 25 to 27 in 3e965b0

	scores=temp(
	"results/balancing_selection/scikit-allel/{species}/1pop/{ppl}/{method}/{window}_{step}/chr{i}.{method}.scores.txt"
	),

[xin-huang]

can Snakefile be simplified?

[xin-huang]

delta tajima's d -> moving_delta_tajima_d

[xin-huang]

refactor

selscape/config/main.yaml

Lines 11 to 12 in b891daa

	genome_annotation: "examples/data/Human/annotation/Human.gtf.gz"
	gene2go: "examples/data/Human/annotation/gene2go.gz"

[nomis-c]

selscape/docs/index.md

Line 24 in 6c285cf

- pydantic=2.5.0

pydantic needs to be removed from selscape/docs/index.md