biopipen 0.32.3__py3-none-any.whl → 0.33.0__py3-none-any.whl

{biopipen-0.32.3.dist-info → biopipen-0.33.0.dist-info}/RECORD

@@ -1,35 +1,35 @@
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 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
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 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
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 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
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 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
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@@ -53,8 +53,8 @@ biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaas
 biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
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 biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo7AD-gK6g,491
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 biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
 biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
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@@ -67,6 +67,7 @@ biopipen/reports/snp/PlinkHWE.svelte,sha256=nes-NTwatoxvLoRBCg6jPp0fSg5kZZkVngUR
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@@ -74,65 +75,69 @@ biopipen/reports/tcr/TCRClusterStats.svelte,sha256=YGK5_Vp85QmUJZO1ZGtg1IWBsh9o-
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@@ -235,9 +241,10 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=xVuBa38SPQ7qSSynDwvyuYljs1M0yKaIhC
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 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
 biopipen/scripts/tcr/TESSA_source/BriseisEncoder.py,sha256=z4_Q_6StymffuUGGjHP1-B3aTsXtamKao5Q1-Kg9has,6831
@@ -251,46 +258,48 @@ biopipen/scripts/tcr/TESSA_source/update.R,sha256=kVrf6zgIkhhiQ2O55XGmxm_DGBKSpc
 biopipen/scripts/tcr/TESSA_source/utility.R,sha256=6qbkMV7yp4bgQe718QiASQUAgOE2euiLgAXOeSqrvHQ,374
 biopipen/scripts/tcr/VJUsage.R,sha256=LjHEbAHW3WriCYiM9-T6Esd4jc6pnoiSxBKTN_YA490,437
 biopipen/scripts/tcr/immunarch-patched.R,sha256=6OAaV6arDVSI409VHuh1oMCuxlMQp-EaM-kkF-sTlCI,7007
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-biopipen/scripts/vcf/BcftoolsView.py,sha256=Sj3KkYPpwQFo5kmZC5MRxItrSE5KVZi0jNYrRFck3Ow,2465
+biopipen/scripts/tcr/vdjtools-patch.sh,sha256=-gJFPVqzzFLdet3q2hccB8gSztRawLV1AnqNp1ZzHOg,568
+biopipen/scripts/vcf/BcftoolsAnnotate.py,sha256=12-VUSP0kl0iyxvahhiu1CDyYJ9nTgGo5RWWVKhkBN8,2615
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+biopipen/scripts/vcf/BcftoolsMerge.py,sha256=KpCcEKNtDOEn8n0qSyWpi-lFv1qjnwqJRUlWNrXaqaU,989
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 biopipen/scripts/vcf/TruvariBench.sh,sha256=5M7lZhO4laNJvCVCHudf8DYArKNXoiPWuSkXgRi2t_A,908
 biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=rdNNIPoiwqnK6oEOlQUUhnL1MF958W_nDjRCkA5ubz4,1516
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 biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/utils/gene.py,sha256=ToRgAPYc8E72Hm6uYi84ImQaRMPZp5rN7O4CxK7vCag,4477
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 biopipen/utils/plot.R,sha256=ijqVU68W_jl27YHSuHSFekOSvTus97mRCqpbri_2an4,5880
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{biopipen-0.32.3.dist-info → biopipen-0.33.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.1
 Root-Is-Purelib: true
 Tag: py3-none-any

biopipen/scripts/scrna/SeuratClusterStats-hists.R

@@ -1,144 +0,0 @@
-# Loaded variables: srtfile, outdir, srtobj
-
-# hists_defaults <- {{envs.hists_defaults | r: todot="-"}}
-# hists <- {{envs.hists | r: todot="-", skip=1}}
-log_info("hists:")
-
-do_one_hists <- function(m, case, odir, h1, each = NULL) {
-    ofile <- file.path(odir, paste0(slugify(h1), ifelse(is.null(each), "", paste0("-", slugify(each))), ".png"))
-    ofile_pdf <- gsub(".png$", ".pdf", ofile)
-
-    p <- ggplot(m, aes(x=!!sym(case$x))) +
-        geom_histogram(
-            bins = case$bins,
-            fill = "white",
-            color = "#3a9ddc",
-            stat = ifelse(is.numeric(m[[case$x]]), "bin", "count")
-        ) +
-        theme_prism() +
-        xlab(case$x) +
-        ylab("Number of cells")
-
-    if (!is.null(case$cells_by)) {
-        p <- p + facet_wrap(vars(!!sym(case$cells_by)), ncol = case$ncol, drop = FALSE)
-        ngroups <- length(unique(m[[case$cells_by]]))
-    } else {
-        ngroups <- 1
-    }
-
-    if (!is.null(case$plus) && length(case$plus) > 0) {
-        for (pl in case$plus) {
-            p <- p + eval(parse(text=pl))
-        }
-    }
-
-    devpars <- case$devpars
-    if (is.null(devpars$res)) { devpars$res <- 100 }
-    if (is.null(devpars$width)) {
-        devpars$width <- ifelse(ngroups == 1, 600, 300 * min(ngroups, case$ncol)) }
-    if (is.null(devpars$height)) {
-        devpars$height <- ifelse(ngroups == 1, 300, 150 * ceiling(ngroups / case$ncol))
-    }
-    png(ofile, width=devpars$width, height=devpars$height, res=devpars$res)
-    print(p)
-    dev.off()
-
-    pdf(ofile_pdf, width=devpars$width / devpars$res, height=devpars$height / devpars$res)
-    print(p)
-    dev.off()
-
-    # Add report
-    if (!is.null(each)) {
-        add_report(
-            list(src = ofile, descr = first(m[[case$each]]), download = ofile_pdf),
-            h1 = h1,
-            ui = "table_of_images"
-        )
-    } else {
-        add_report(
-            list(kind = "image", src = ofile, download = ofile_pdf),
-            h1 = h1
-        )
-    }
-}
-
-if (is.null(hists) || length(hists) == 0) {
-    log_warn("- no cases specified, skipping ...")
-} else {
-
-    for (name in names(hists)) {
-        hists[[name]] <- list_update(hists_defaults, hists[[name]])
-        case <- hists[[name]]
-
-        odir <- file.path(outdir, "hists", slugify(name))
-        dir.create(odir, recursive=TRUE, showWarnings=FALSE)
-
-        h1 <- name
-        if (!is.null(case$subset)) {
-            meta <- srtobj@meta.data %>% filter(!!rlang::parse_expr(case$subset))
-        } else {
-            meta <- srtobj@meta.data
-        }
-
-        if (is.null(case$x)) { stop("`x` must be specified for hists.") }
-
-        meta <- meta %>% drop_na(!!sym(case$x))
-        if (!is.null(case$cells_by)) { meta <- meta %>% drop_na(!!sym(case$cells_by)) }
-        if (!is.null(case$each)) { meta <- meta %>% drop_na(!!sym(case$each)) }
-        if (!is.null(case$x_order) && length(case$x_order) > 0) {
-            meta <- meta %>% filter(!!sym(case$x) %in% case$x_order) %>%
-                arrange(match(!!sym(case$x), case$x_order))
-        }
-        if (!is.null(case$cells_order) && length(case$cells_order) > 0) {
-            if (is.null(case$cells_by)) { stop("`cells_by` must be specified for `cells_order`.") }
-            meta <- meta %>% filter(!!sym(case$cells_by) %in% case$cells_order) %>%
-                arrange(match(!!sym(case$cells_by), case$cells_order))
-        } else if (!is.null(case$cells_orderby)) {
-            meta <- meta %>% arrange(!!parse_expr(case$cells_orderby))
-            cell_groups <- meta %>% pull(!!sym(case$cells_by)) %>% unique()
-            meta <- meta %>% filter(!!sym(case$cells_by) %in% cell_groups[1:case$cells_n])
-            meta[[case$cells_by]] <- factor(meta[[case$cells_by]], levels=cell_groups[1:case$cells_n])
-        }
-
-        if (!is.null(case$each)) {
-            eachs <- meta %>% pull(!!sym(case$each)) %>% unique()
-            add_report(
-                list(
-                    kind = "descr",
-                    content = paste0(
-                        "Histogram showing number of cells ",
-                        ifelse(is.null(case$cells_by), "", paste0("by <code>", case$cells_by, "</code> ")),
-                        "in each <code>",
-                        case$each,
-                        "</code> along <code>",
-                        case$x,
-                        "</code>"
-                    )
-                ),
-                h1 = h1
-            )
-            for (each in eachs) {
-                log_info("- Case: {h1} - {each} ...")
-                m <- meta %>% filter(!!sym(case$each) == each)
-                do_one_hists(m, case, odir, h1, each)
-            }
-        } else {
-            log_info("- Case: {h1} ...")
-            add_report(
-                list(
-                    kind = "descr",
-                    content = paste0(
-                        "Histogram showing number of cells ",
-                        ifelse(is.null(case$cells_by), "", paste0("by <code>", case$cells_by, "</code> ")),
-                        "along <code>",
-                        case$x,
-                        "</code>"
-                    )
-                ),
-                h1 = h1
-            )
-            do_one_hists(meta, case, odir, h1)
-        }
-    }
-
-}