biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -1,55 +0,0 @@
-{% from "utils/misc.liq" import report_jobs -%}
-{% from "utils/gsea.liq" import enrichr_report -%}
-<script>
-    import { Image, DataTable } from "$libs";
-    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-</script>
-
-
-{%- macro report_job(job, h=1) -%}
-    {%- set secdirs = job.out.outdir | glob: "*" -%}
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- for casedir in secdirs[0] | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{casedir | basename | escape}}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape}} - {{casedir | basename | escape}}</h{{h}}>
-            {%- endif -%}
-
-            <h{{h+1}}>Markers</h{{h+1}}>
-            <DataTable
-                src={{ casedir | joinpaths: "exprn.txt" | quote }}
-                data={ {{ casedir | joinpaths: "exprn.txt" | datatable: sep="\t", nrows=100 }} }
-                />
-
-            <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-            {{ enrichr_report(casedir) }}
-
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- for casedir in secdir | glob: "*" -%}
-                <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-
-                <h{{h+2}}>Markers</h{{h+2}}>
-                <DataTable
-                    src={{ casedir | joinpaths: "exprn.txt" | quote }}
-                    data={ {{ casedir | joinpaths: "exprn.txt" | datatable: sep="\t", nrows=100 }} }
-                    />
-
-                <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                {{ enrichr_report(casedir) }}
-
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-  <h1>{{job.in.srtobj | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte

@@ -1,31 +0,0 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-{% from "utils/gsea.liq" import fgsea_report, gsea_report -%}
-
-<script>
-  import { Image, DataTable } from "$libs";
-</script>
-
-{%- macro report_job(job, h=2) -%}
-  {%  for groupdir in job.out.outdir | glob: "*" %}
-    <h{{h}}>{{groupdir | basename}}</h{{h}}>
-    {%- set dsdirs = groupdir | glob: "*" -%}
-    {% for dsdir in groupdir | glob: "*" %}
-        <h{{h+1}}>{{ dsdir | basename }}</h{{h+1}}>
-        {% if envs.fgsea %}
-            {% if dsdir | joinpaths: "fgsea.txt" | isfile %}
-                {{ fgsea_report(dsdir, h+2, envs, envs.top) }}
-            {% else %}
-                <p>Not enough events.</p>
-            {% endif %}
-        {% else %}
-            {{ gsea_report(dsdir, h+2, envs, envs.top) }}
-        {% endif %}
-    {% endfor %}
-  {% endfor %}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-  <h1>{{job.in.sobjfile | stem | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/utils/gsea.liq

@@ -1,110 +0,0 @@
-{% from "utils/misc.liq" import table_of_images -%}
-
-{%- macro fgsea_report_script() -%}
-import { Image, DataTable } from "$libs";
-{%- endmacro -%}
-
-{%- macro fgsea_report(fgsea_dir, h, envs, nrows=100) -%}
-{%- addfilter splitgenes -%}
-def splitgenes(data):
-    for dat in data:
-        dat["leadingEdge"] = dat["leadingEdge"].replace(",", " ")
-    return json_dumps(data)
-{%- endaddfilter -%}
-
-<h{{h}}>Enrichment table</h{{h}}>
-<Image src={{ fgsea_dir | joinpaths: "gsea_table.png" | quote }} />
-
-{% set data = fgsea_dir | joinpaths: "fgsea.txt" | datatable: sep="\t", nrows=nrows | json_loads %}
-
-<h{{h}}>Enrichment pathways</h{{h}}>
-<DataTable src={{ fgsea_dir | joinpaths: "fgsea.txt" | quote }}
-    data={ {{ data | splitgenes: }} }
-    pageSize={10} />
-
-<h{{h}}>Enrichment plot of pathways</h{{h}}>
-{%- python -%}
-import os
-def fgsea_plots(pathways, fgsea_dir):
-    out = []
-    for pathway in pathways:
-        pathway = pathway.replace("/", "-")
-        pwfig = joinpaths(fgsea_dir, f"fgsea_{pathway}.png")
-        if os.path.exists(pwfig):
-            out.append(pwfig)
-    return out
-{%- endpython -%}
-{{ table_of_images(
-    fgsea_plots(liquid_map(data, "pathway"), fgsea_dir),
-    liquid_map(data, "pathway"),
-    table_width=75
-) }}
-
-{%- endmacro -%}
-
-
-{%- macro gsea_report(gsea_dir, h, envs, nrows=100) -%}
-<h{{h}}>Global view</h{{h}}>
-
-<embed src={{gsea_dir | joinpaths: "*.global.plots.pdf" | glob | first | quote}}
-    width="100%"
-    height="1000"
-    type="application/pdf" />
-
-<h{{h}}>Summary</h{{h}}>
-{% for sumfile in gsea_dir | joinpaths: "*.SUMMARY.RESULTS.REPORT.*.txt" | glob %}
-{%   set klass = stem(sumfile).split(".")[-1] %}
-<h{{h+1}}>{{klass}}</h{{h+1}}>
-<DataTable data={ {{sumfile | datatable: sep="\t", nrows=nrows}} } />
-{% endfor %}
-
-<h{{h}}>Enrichment details</h{{h}}>
-{% set cutoff = envs.get("fdr.q.val.threshold", envs.get("fdr_q_val_threshold", 0.25)) %}
-{% for sumfile in gsea_dir | joinpaths: "*.SUMMARY.RESULTS.REPORT.*.txt" | glob %}
-{%   set klass = stem(sumfile).split(".")[-1] %}
-<h{{h+1}}>{{klass}}</h{{h+1}}>
-{%   set sumdata = sumfile | datatable: sep="\t" | json_loads %}
-{%   set has_signif = [] %}
-{%   for row in sumdata %}
-{%      if row["FDR_q_val"] < cutoff %}
-{%          set _ = has_signif.append(1) %}
-<embed src={{gsea_dir | joinpaths: "*." + row["GS"] + ".plot." + klass + ".*.pdf" | glob | first | quote}}
-    width="100%"
-    height="700"
-    type="application/pdf" />
-{%      endif %}
-{%   endfor %}
-{%   if len(has_signif) == 0 %}
-<Tile>No significantly (FDR_q_val &lt; {{cutoff}}) enriched pathways found.</Tile>
-{%   endif %}
-{% endfor %}
-
-{%- endmacro -%}
-
-
-{%- macro enrichr_report_script() -%}
-import { Image, DataTable } from "$libs";
-import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-{%- endmacro -%}
-
-{%- macro enrichr_report(enrichr_dir) -%}
-<Tabs>
-    {% for enrtxt in enrichr_dir | glob: "Enrichr-*.txt"  %}
-        {% set db = enrtxt | stem | replace: "Enrichr-", "" %}
-        <Tab label="{{db}}" title="{{db}}" />
-    {% endfor %}
-    <div slot="content">
-        {% for enrtxt in enrichr_dir | glob: "Enrichr-*.txt" %}
-            {% set db = enrtxt | stem | replace: "Enrichr-", "" %}
-            <TabContent>
-                <Image src={{enrichr_dir | joinpaths: "Enrichr-" + db + ".png" | quote}} />
-                <DataTable
-                    src={{ enrtxt | quote }}
-                    data={ {{ enrtxt | datatable: sep="\t", nrows=100 }} }
-                    />
-            </TabContent>
-        {% endfor %}
-    </div>
-</Tabs>
-{%- endmacro -%}
-

biopipen/scripts/bcftools/BcftoolsAnnotate.py

@@ -1,42 +0,0 @@
-from os import path
-
-from biopipen.utils.reference import tabix_index
-from biopipen.utils.misc import dict_to_cli_args, run_command
-
-infile = {{in.infile | repr}}  # pyright: ignore
-annfile = {{(in.annfile or envs.annfile) | repr}}  # pyright: ignore
-outfile = {{out.outfile | repr}}  # pyright: ignore
-joboutdir = {{job.outdir | repr}}  # pyright: ignore
-bcftools = {{envs.bcftools | repr}}  # pyright: ignore
-tabix = {{envs.tabix | repr}}  # pyright: ignore
-ncores = {{envs.ncores | repr}}  # pyright: ignore
-cols = {{envs.cols | repr}}  # pyright: ignore
-header = {{envs.header | repr}}  # pyright: ignore
-args = {{envs.args | repr}}  # pyright: ignore
-
-args[""] = bcftools
-args["_"] = tabix_index(infile, "vcf")
-args["o"] = outfile
-args["threads"] = ncores
-
-if annfile:
-    abname = path.basename(annfile)
-    ext = path.splitext(
-        abname[:-3] if abname.endswith('.gz') else abname
-    )[-1][1:]
-    args["a"] = tabix_index(annfile, ext, tabix)
-
-if cols and isinstance(cols, list):
-    args["c"] = ",".join(cols)
-
-if header:
-    if not isinstance(header, list):
-        header = [header]
-
-    headerfile = path.join(joboutdir, "header.txt")
-    with open(headerfile, "w") as fh:
-        for head in header:
-            fh.write(f"{head}\n")
-    args["h"] = headerfile
-
-run_command(dict_to_cli_args(args, dashify=True), fg=True)

biopipen/scripts/bcftools/BcftoolsFilter.py

@@ -1,79 +0,0 @@
-import shutil
-from pathlib import Path
-from hashlib import md5
-
-from biopipen.core.filters import dict_to_cli_args, run_command
-
-infile = {{in.infile | repr}}  # pyright: ignore
-outfile = {{out.outfile | repr}}  # pyright: ignore
-bcftools = {{envs.bcftools | repr}}  # pyright: ignore
-keep = {{envs.keep | repr}}  # pyright: ignore
-args = {{envs.args | repr}}  # pyright: ignore
-ncores = {{envs.ncores | repr}}  # pyright: ignore
-tmpdir = {{envs.tmpdir | repr}}  # pyright: ignore
-includes = {{envs.includes | repr}}  # pyright: ignore
-excludes = {{envs.excludes | repr}}  # pyright: ignore
-
-args[""] = bcftools
-args["_"] = infile
-args["o"] = outfile
-args["threads"] = ncores
-if "O" not in args and "output-type" not in args:
-    args["O"] = "z" if infile.endswith(".gz") else "v"
-if "m" not in args and "mode" not in args:
-    args["m"] = "+"
-
-tmpdir = (
-    Path(tmpdir) / f"biopipen-bcftoolsfilter-{md5(infile.encode()).hexdigest()}"
-)
-tmpdir.mkdir(parents=True, exist_ok=True)
-# a.vcf.gz -> a
-# a.vcf -> a
-stem = Path(infile).stem
-if stem.endswith(".vcf"):
-    stem = stem[:-4]
-# .vcf.gz
-# .gz
-ext = Path(infile).name[len(stem):]
-
-FILTER_INDEX = [1]
-
-def handle_filter(vcf, fname, filt, flag):
-    print("- Handling filter ", fname, ": ", filt, " ...")
-
-    arguments = args.copy()
-    arguments[flag] = filt
-    arguments["_"] = vcf
-    arguments["o"] = tmpdir / f"{stem}.{fname}{ext}"
-    if keep:
-        arguments["s"] = fname
-
-    run_command(dict_to_cli_args(arguments, dashify=True), fg=True)
-    return arguments["o"]
-
-
-def normalize_expr(expr, flag):
-    out = {}
-    if not expr:
-        return out
-    if isinstance(expr, list):
-        for ex in expr:
-            out[f"FILTER{FILTER_INDEX[0]}"] = (ex, flag)
-            FILTER_INDEX[0] += 1
-    elif isinstance(expr, dict):
-        for name, ex in expr.items():
-            out[name] = (ex, flag)
-    else: # str
-        out[f"FILTER{FILTER_INDEX[0]}"] = (expr, flag)
-        FILTER_INDEX[0] += 1
-    return out
-
-includes = normalize_expr(includes, "include")
-excludes = normalize_expr(excludes, "exclude")
-includes.update(excludes)
-
-# bcftools can be only done once at one filter
-for fname, (filt, flag) in includes.items():
-    infile = handle_filter(infile, fname, filt, flag)
-
-shutil.copy2(infile, outfile)

biopipen/scripts/bcftools/BcftoolsSort.py

@@ -1,19 +0,0 @@
-from biopipen.utils.misc import run_command, dict_to_cli_args
-
-infile = {{in.infile | quote}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
-bcftools = {{envs.bcftools | quote}}  # pyright: ignore
-gz = {{envs.gz | repr}}  # pyright: ignore
-args = {{envs.args | repr}}  # pyright: ignore
-tmpdir = {{envs.tmpdir | quote}}  # pyright: ignore
-index = {{envs.index | repr}}  # pyright: ignore
-
-args[""] = bcftools
-args["_"] = infile
-args["o"] = outfile
-args["O"] = "z" if gz or index else "v"
-
-run_command(dict_to_cli_args(args, dashify=True), fg=True)
-
-if index:
-    run_command([bcftools, "index", outfile], fg=True)

biopipen/scripts/gene/GeneNameConversion.py

@@ -1,66 +0,0 @@
-import pandas
-from datar.all import c, right_join, select, relocate
-from biopipen.utils.gene import gene_name_conversion
-
-infile = {{in.infile | quote}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
-inopts = {{envs.inopts | repr}}  # pyright: ignore
-outopts = {{envs.outopts | repr}}  # pyright: ignore
-notfound = {{envs.notfound | repr}}  # pyright: ignore
-genecol = {{envs.genecol | repr}}  # pyright: ignore
-output = {{envs.output | repr}}  # pyright: ignore
-infmt = {{envs.infmt | repr}}  # pyright: ignore
-outfmt = {{envs.outfmt | repr}}  # pyright: ignore
-species = {{envs.species | quote}}  # pyright: ignore
-
-df = pandas.read_csv(infile, **inopts)
-
-if isinstance(genecol, int):
-    genes = df.iloc[:, genecol]
-else:
-    genes = df.loc[:, genecol]
-
-colname = genes.name
-genes = genes.tolist()
-
-#        query  `outfmt`
-#     <object> <object>
-# 0  1255_g_at   GUCA1A
-# 1    1316_at     THRA
-# 2    1320_at   PTPN21
-# 3    1294_at  MIR5193
-converted = gene_name_conversion(
-    genes=genes,
-    species=species,
-    infmt=infmt,
-    outfmt=outfmt,
-    notfound=notfound,
-)
-converted.columns = [colname] + converted.columns[1:].tolist()
-
-if output == "only":
-    out = converted
-
-elif output == "keep":
-    out = df >> right_join(converted, by=colname, suffix=["", "_converted"])
-
-elif output == "drop":
-    out = df >> right_join(
-        converted,
-        by=colname, suffix=["", "_converted"]
-    ) >> select(~c(colname))
-
-elif output == "replace":
-    out = df >> right_join(
-        converted, by=colname, suffix=["", "_converted"]
-    )
-    converted_cols = out.columns[-len(converted.columns)+1:].tolist()
-    pos = df.columns.get_indexer([colname])[0]
-    out = out >> relocate(
-        converted_cols, _after=pos+1
-    ) >> select(~c(colname))
-
-else:
-    raise ValueError(f"Unknown output mode: {output}.")
-
-out.to_csv(outfile, **outopts)

biopipen/scripts/scrna/ExprImpution-alra.R

@@ -1,32 +0,0 @@
-source("{{biopipen_dir}}/utils/misc.R")
-
-library(SeuratWrappers)
-library(Seurat)
-
-infile = {{in.infile | r}}
-outfile = {{out.outfile | r}}
-envs = {{envs.alra_args | r}}
-
-print("Loading Seurat object")
-sobj = readRDS(infile)
-DefaultAssay(sobj) <- "RNA"
-
-print("Imputing expression values, using ALRA")
-envs$object = sobj
-sobj = do_call(RunALRA, envs)
-
-# sobj = RunALRA(sobj)
-print("Renaming assays")
-sobj = RenameAssays(sobj, RNA = "UNIMPUTED_RNA")
-sobj = RenameAssays(sobj, alra = "RNA")
-DefaultAssay(sobj) <- "RNA"
-
-attr(sobj, "impute") = "alra"
-print("Saving Seurat object")
-saveRDS(sobj, outfile)
-
-# choosek_plot_file = file.path(dirname(outfile), "choosek.png")
-# png(choosek_plot_file, width = 1200, height = 1000, res = 100)
-# p = ALRAChooseKPlot(sobj)
-# print(p)
-# dev.off()

biopipen/scripts/scrna/ExprImpution-rmagic.R

@@ -1,29 +0,0 @@
-
-tryCatch({
-    # in order to load Rmagic
-    workdir = {{job.outdir | r}}
-    conda_prefix = Sys.getenv("CONDA_PREFIX")
-    setwd(workdir)
-    file.symlink(conda_prefix, "miniconda3")
-}, error=function(e) {})
-
-python = {{envs.rmagic_args.python | r}}
-Sys.setenv(RETICULATE_PYTHON = Sys.which(python))
-# reticulate::use_python(python)
-
-library(Rmagic)
-library(Seurat)
-
-infile = {{in.infile | r}}
-outfile = {{out.outfile | r}}
-
-sobj = readRDS(infile)
-DefaultAssay(sobj) <- "RNA"
-
-sobj = magic(sobj)
-sobj = RenameAssays(sobj, RNA = "UNIMPUTED_RNA", MAGIC_RNA = "RNA")
-
-DefaultAssay(sobj) <- "RNA"
-
-attr(sobj, "impute") = "rmagic"
-saveRDS(sobj, outfile)

biopipen/scripts/scrna/ExprImpution.R

@@ -1,7 +0,0 @@
-{% if envs.tool == "rmagic" %}
-{% include biopipen_dir + "/scripts/scrna/ExprImpution-rmagic.R" %}
-{% elif envs.tool == "scimpute" %}
-{% include biopipen_dir + "/scripts/scrna/ExprImpution-scimpute.R" %}
-{% elif envs.tool == "alra" %}
-{% include biopipen_dir + "/scripts/scrna/ExprImpution-alra.R" %}
-{% endif %}

biopipen/scripts/scrna/GeneExpressionInvistigation.R

@@ -1,132 +0,0 @@
-source("{{biopipen_dir}}/utils/io.R")
-source("{{biopipen_dir}}/utils/misc.R")
-source("{{biopipen_dir}}/utils/plot.R")
-library(Seurat)
-library(dplyr)
-library(tidyr)
-library(tibble)
-library(rlang)
-library(ggplot2)
-library(ggprism)
-library(ComplexHeatmap)
-
-srtobjfile = {{in.srtobj | quote}}
-genefile = {{in.genefile | r}}
-outdir = {{out.outdir | quote}}
-gopts = {{envs.gopts | r}}
-{% if in.configfile %}
-config = {{in.configfile | toml_load | r}}
-{% set config = in.configfile | toml_load %}
-{% else %}
-config = {{envs.config | r}}
-{% set config = envs.config %}
-{% endif %}
-
-sobj = readRDS(srtobjfile)
-genes = read.table.opts(genefile, gopts)
-if (ncol(genes) == 1) {
-    genes$.Name = genes[[1]]
-}
-colnames(genes) = c("Gene", "Name")
-
-if (!is.null(config$mutaters)) {
-    expressions = list()
-    for (key in names(config$mutaters)) {
-        expressions[[key]] = parse_expr(config$mutaters[[key]])
-    }
-    sobj@meta.data = mutate(sobj@meta.data, !!!expressions)
-}
-
-if (!is.null(config$subset)) {
-    sobj = subset(sobj, subset = {{config.subset}})
-}
-
-DefaultAssay(sobj) <- "RNA"
-sobj = NormalizeData(sobj)
-
-exprs = as.data.frame(
-    GetAssayData(sobj, slot = "data", assay = "RNA")
-)[genes$Gene,,drop=F]
-rownames(exprs) = genes$Name
-exprs = rownames_to_column(exprs, "Gene")
-
-plot_heatmap = function(plotconf, outfile) {
-    plotdata = exprs %>%
-        pivot_longer(
-            names(exprs)[2:ncol(exprs)],
-            names_to = "Barcode",
-            values_to = "Log_Expression"
-        )
-    metadata = sobj@meta.data[plotdata$Barcode,,drop=F]
-    plotdata = cbind(plotdata, metadata)
-    plotdata = plotdata %>%
-        group_by(Gene, !!sym(config$groupby)) %>%
-        summarise(Log_Expression = mean(Log_Expression)) %>%
-        pivot_wider(names_from = config$groupby, values_from = "Log_Expression") %>%
-        column_to_rownames("Gene")
-
-    given_genes = rownames(plotdata)
-    plotdata = plotdata[complete.cases(plotdata),,drop=FALSE]
-    invalid_genes = setdiff(given_genes, rownames(plotdata))
-    if (length(invalid_genes) > 0) {
-        warning(
-            paste(
-                "The following genes were not found in the data:",
-                invalid_genes
-            )
-        )
-    }
-
-    devpars = list(res=plotconf$res, width=plotconf$width, height=plotconf$height)
-    plotconf$res = NULL
-    plotconf$width = NULL
-    plotconf$height = NULL
-
-    for (name in names(plotconf)) {
-        plotconf[[name]] = parse_expr(plotconf[[name]])
-    }
-
-    plotHeatmap(
-        plotdata,
-        plotconf,
-        devpars = devpars,
-        outfile = outfile
-    )
-}
-
-plot_boxplot = function(plotconf, outfile) {
-    plotdata = exprs %>%
-        pivot_longer(
-            names(exprs)[2:ncol(exprs)],
-            names_to = "Barcode",
-            values_to = "Log_Expression"
-        )
-    metadata = sobj@meta.data[plotdata$Barcode,,drop=F]
-    plotdata = cbind(plotdata, metadata)
-
-    cols = if (is.null(plotconf$ncol)) 3 else plotconf$ncol
-    p = ggplot(plotdata) +
-        geom_boxplot(aes_string(x=config$groupby, y="Log_Expression", fill=config$groupby)) +
-        facet_wrap(~Gene, ncol=cols) +
-        theme_prism(axis_text_angle = 90) + theme(legend.position = "none") +
-        xlab("")
-
-    devpars = list(filename = outfile, res = plotconf$res, width = plotconf$width, height = plotconf$height)
-    do_call(png, devpars)
-    print(p)
-    dev.off()
-}
-
-
-for (plottype in names(config$plots)) {
-    plotconf = config$plots[[plottype]]
-    if (plottype == "heatmap") {
-        plotfile = file.path(outdir, "heatmap.png")
-        plot_heatmap(plotconf, plotfile)
-    } else if (plottype == "boxplot") {
-        plotfile = file.path(outdir, "boxplot.png")
-        plot_boxplot(plotconf, plotfile)
-    } else {
-        stop(paste("Unknown plot type:", plottype))
-    }
-}

biopipen/scripts/scrna/Write10X.R

@@ -1,11 +0,0 @@
-library(DropletUtils)
-library(Seurat)
-
-srtobjfile = {{in.srtobj | r}}
-outdir = {{out.outdir | r}}
-version = {{envs.version | r}}
-
-srtobj = readRDS(srtobjfile)
-counts = GetAssayData(object = srtobj, slot = "counts")
-
-write10xCounts(outdir, counts, version = version, overwrite = TRUE)