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

biopipen/scripts/tcr/CDR3Clustering.R

@@ -0,0 +1,343 @@
+library(dplyr)
+library(tidyr)
+library(tibble)
+library(glue)
+library(biopipen.utils)
+
+screpfile <- {{in.screpfile | r}}
+outdir <- normalizePath({{job.outdir | r}})
+outfile <- {{out.outfile | r}}
+
+tool <- {{envs.tool | r}}
+python <- {{envs.python | r}}
+within_sample <- {{envs.within_sample | r}}
+args <- {{envs.args | r}}
+chain <- {{envs.chain | r}}
+type <- {{envs.type | r}}
+
+setwd(outdir)
+
+log <- get_logger()
+
+log$info("Reading input file ...")
+obj <- read_obj(screpfile)
+is_seurat <- inherits(obj, "Seurat")
+
+
+get_type <- function() {
+    if (!is_seurat) {
+        for (sample in names(obj)) {
+            for (gene in obj[[sample]]$CTgene) {
+                if (grepl("^TRB", gene) || grepl("^TRG", gene) || grepl("^TRA", gene) || grepl("^TRD", gene)) {
+                    return("TCR")
+                } else if (grepl("^IGH", gene) || grepl("^IGK", gene) || grepl("^IGL", gene)) {
+                    return("BCR")
+                }
+            }
+        }
+    } else {
+        for (gene in obj@meta.data$CTgene) {
+            if (grepl("^TRB", gene) || grepl("^TRG", gene) || grepl("^TRA", gene) || grepl("^TRD", gene)) {
+                return("TCR")
+            } else if (grepl("^IGH", gene) || grepl("^IGK", gene) || grepl("^IGL", gene)) {
+                return("BCR")
+            }
+        }
+    }
+    stop("Cannot determine the type of the data (TCR or BCR). Please set envs.type to 'TCR' or 'BCR'.")
+}
+
+if (type == "auto") {
+    type <- get_type()
+    log$info("Auto-detected data type: {type}")
+}
+
+get_cdr3aa_df <- function() {
+    if (!is_seurat) {
+        out <- NULL
+        for (sample in names(obj)) {
+            df <- data.frame(
+                Sample = sample,
+                Barcode = obj[[sample]]$barcode
+            )
+            if (chain == "both") {
+                df$CDR3.aa <- obj[[sample]]$CTaa
+            } else if ((type == "BCR" && chain == "heavy") || (type == "TCR" && chain == "light")) {
+                df$CDR3.aa <- obj[[sample]]$cdr3_aa1
+            } else if ((type == "BCR" && chain == "light") || (type == "TCR" && chain == "heavy")) {
+                df$CDR3.aa <- obj[[sample]]$cdr3_aa2
+            } else {
+                stop(paste("Unknown chain:", chain, "for", type))
+            }
+            out <- rbind(out, df)
+        }
+    } else {
+        out <- obj@meta.data
+        out$Barcode <- rownames(out)
+        out <- out %>% filter(!is.na(CTaa))
+        if (grepl("_", out$CTaa[1])) {
+            if (chain == "both") {
+                out$CDR3.aa <- out$CTaa
+            } else {
+                out <- separate(out, CTaa, into = c("first", "second"), sep = "_")
+                if ((type == "BCR" && chain == "heavy") || (type == "TCR" && chain == "light")) {
+                    out$CDR3.aa <- out$first
+                } else if ((type == "BCR" && chain == "light") || (type == "TCR" && chain == "heavy")) {
+                    out$CDR3.aa <- out$second
+                } else {
+                    stop(paste("Unknown chain:", chain, "for", type))
+                }
+            }
+        } else {
+            out$CDR3.aa <- out$CTaa
+        }
+        out <- select(out, Sample, Barcode, CDR3.aa)
+    }
+
+    # Sample, Barcode, CDR3.aa
+    out
+}
+cdr3aa_df = get_cdr3aa_df()
+
+prepare_clustcr = function(clustcr_dir) {
+    clustering_args = ""
+    for (name in names(args)) {
+        value = args[[name]]
+        if (is.logical(value)) {
+            value = tools::toTitleCase(as.character(value))
+        } else if (is.character(value)) {
+            value = paste0("'", value, "'")
+        }
+        clustering_args = paste(name, "=", value)
+    }
+    clustcr_source = '
+import sys
+import atexit
+
+import pandas as pd
+from scipy import sparse as scipy_sparse
+
+
+@atexit.register
+def clustcr_exit():
+    import pandas as pd
+    import numpy
+    import scipy
+    import sklearn
+    import matplotlib
+    sys.stderr.write("Session info:\\n")
+    sys.stderr.write(f"- pandas: {pd.__version__}\\n")
+    sys.stderr.write(f"- numpy: {numpy.__version__}\\n")
+    sys.stderr.write(f"- scipy: {scipy.__version__}\\n")
+    sys.stderr.write(f"- sklearn: {sklearn.__version__}\\n")
+    sys.stderr.write(f"- matplotlib: {matplotlib.__version__}\\n")
+
+
+# Monkey-patch scipy.sparse.isspmatrix to adopt latest scipy v1.14
+# If not, an error is raised:
+#   numpy.linalg.LinAlgError: 0-dimensional array given.
+#   Array must be at least two-dimensional
+scipy_sparse.isspmatrix = lambda x: isinstance(
+    x,
+    (
+        scipy_sparse.spmatrix,
+        scipy_sparse.csr_array,
+        scipy_sparse.csr_matrix,
+        scipy_sparse.csc_array,
+        scipy_sparse.csc_matrix,
+    ),
+)
+
+
+import clustcr  # noqa: #402
+
+clustcr_dir, clustcr_infile = sys.argv[1:3]
+cdr3df = pd.read_csv(clustcr_infile, index_col=None)
+cdr3 = cdr3df.iloc[:, 0]
+
+clustering = clustcr.Clustering()
+output = clustering.fit(cdr3)
+output.clusters_df.to_csv(clustcr_dir + "/clusters.txt", sep="\t", index=False)
+'
+    clustcr_file = file.path(clustcr_dir, "_clustcr.py")
+    cat(sprintf(clustcr_source, clustering_args), file=clustcr_file)
+    clustcr_file
+}
+
+clean_clustcr_output = function(clustcr_outfile) {
+    clustcr_out = read.delim2(clustcr_outfile, header=TRUE, row.names = NULL)
+    colnames(clustcr_out) = c("CDR3.aa", "CDR3_Cluster")
+    out = left_join(cdr3aa_df, distinct(clustcr_out), by=c(cdr3seq4clustering = "CDR3.aa")) %>%
+        mutate(
+            CDR3_Cluster = if_else(
+                is.na(CDR3_Cluster),
+                paste0("S_", row_number()),
+                paste0("M_", as.character(CDR3_Cluster))
+            )
+        )
+
+    if (within_sample) {
+        out <- mutate(out, CDR3_Cluster = paste0(Sample, ".", CDR3_Cluster))
+    }
+
+    # This join would result in more rows than dplyr can handle
+    # left_join(cdr3aa_df, out, by = "CDR3.aa")
+    out <- out[match(cdr3aa_df$CDR3.aa, out$CDR3.aa), , drop=FALSE]
+    cbind(cdr3aa_df, out[, setdiff(colnames(out), "CDR3.aa"), drop=FALSE])
+}
+
+run_clustcr = function() {
+    log$info("Running ClusTCR ...")
+    clustcr_dir = file.path(outdir, "ClusTCR_Output")
+    dir.create(clustcr_dir, showWarnings = FALSE)
+    clustcr_file = prepare_clustcr(clustcr_dir)
+    clustcr_input = prepare_input()
+    clustcr_cmd = paste(
+        python,
+        clustcr_file,
+        clustcr_dir,
+        clustcr_input
+    )
+    print("Running:")
+    print(clustcr_cmd)
+    log$debug("- Running command: {clustcr_cmd}")
+    rc = system(clustcr_cmd)
+    if (rc != 0) {
+        quit(status=rc)
+    }
+    clustcr_outfile = file.path(clustcr_dir, "clusters.txt")
+    clean_clustcr_output(clustcr_outfile)
+}
+
+prepare_giana = function() {
+    biopipen_dir <- get_biopipen_dir(python)
+    giana_srcdir = file.path(biopipen_dir, "scripts", "tcr", "GIANA")
+
+    # # The source code of GIANA is downloaded now to giana_srcdir
+    # giana_file = file.path(giana_srcdir, "GIANA.py")
+    # giana4_file = file.path(giana_srcdir, "GIANA4.py")
+    # giana_query = file.path(giana_srcdir, "query.py")
+    # giana_trbv = file.path(giana_srcdir, "Imgt_Human_TRBV.fasta")
+    # if (!file.exists(giana_file)) {
+    #     download.file(paste(giana_repo, "GIANA4.1.py", sep="/"), giana_file)
+    #     download.file(paste(giana_repo, "GIANA4.py", sep="/"), giana4_file)
+    #     download.file(paste(giana_repo, "query.py", sep="/"), giana_query)
+    #     download.file(paste(giana_repo, "Imgt_Human_TRBV.fasta", sep="/"), giana_trbv)
+    # }
+
+    giana_srcdir
+}
+
+prepare_input = function() {
+    cdr3aa_df$cdr3seq4clustering <<- gsub("[^A-Z]", "", cdr3aa_df$CDR3.aa)  # Remove non-amino acid characters
+    cdr3 <- unique(cdr3aa_df$cdr3seq4clustering)
+
+    # cdr3 = distinct(cdr3, aminoAcid, vMaxResolved)
+
+    cdr3file = file.path(outdir, "cdr3.csv")
+    write.table(
+        data.frame(CDR3.aa=cdr3),
+        cdr3file,
+        row.names=FALSE, col.names=TRUE, quote=FALSE
+    )
+    cdr3file
+}
+
+clean_giana_output = function(giana_outfile) {
+    # generate an output file with columns:
+    # CDR3.aa, CDR3_Cluster, V.name, Sample
+    # If sequence doesn't exist in the input file,
+    # Then a unique cluster id is assigned to it.
+    giana_out = read.delim2(giana_outfile, header=FALSE, comment.char = "#", row.names = NULL)[, 1:2, drop=FALSE]
+    colnames(giana_out) = c("CDR3.aa", "CDR3_Cluster")
+    out = left_join(cdr3aa_df, distinct(giana_out), by=c(cdr3seq4clustering = "CDR3.aa")) %>%
+        mutate(
+            CDR3_Cluster = if_else(
+                is.na(CDR3_Cluster),
+                paste0("S_", row_number()),
+                paste0("M_", as.character(CDR3_Cluster))
+            )
+        )
+
+    if (within_sample) {
+        out <- mutate(out, CDR3_Cluster = paste0(Sample, ".", CDR3_Cluster))
+    }
+
+    # This join would result in more rows than dplyr can handle
+    # left_join(cdr3aa_df, out, by = "CDR3.aa")
+    out <- out[match(cdr3aa_df$CDR3.aa, out$CDR3.aa), , drop=FALSE]
+    cbind(cdr3aa_df, out[, setdiff(colnames(out), "CDR3.aa"), drop=FALSE])
+}
+
+run_giana = function() {
+    log$info("Running GIANA ...")
+    giana_srcdir = prepare_giana()
+    giana_input = prepare_input()
+    giana_outdir = file.path(outdir, "GIANA_Output")
+    dir.create(giana_outdir, showWarnings = FALSE)
+    args_str = ""
+    for (argname in names(args)) {
+        argvalue = args[[argname]]
+        if (!startsWith(argname, "-")) {
+            if (nchar(argname) == 1) {
+                argname = paste0("-", argname)
+            } else {
+                argname = paste0("--", argname)
+            }
+        }
+        if (isTRUE(argvalue) || toupper(as.character(argvalue)) == "TRUE") {
+            argvalue = ""
+        } else {
+            argvalue = as.character(argvalue)
+        }
+        args_str = paste(args_str, argname, argvalue)
+    }
+    giana_cmd = paste(
+        python,
+        file.path(giana_srcdir, "GIANA.py"),
+        "-f", giana_input,
+        "-o", giana_outdir,
+        "-v", # TRBV mutation not supported
+        args_str
+    )
+    print("Running:")
+    print(giana_cmd)
+    log$debug("- Running command: {giana_cmd}")
+    rc = system(giana_cmd)
+    if (rc != 0) {
+        quit(status=rc)
+    }
+    giana_outfile = file.path(giana_outdir, "cdr3--RotationEncodingBL62.txt")
+    clean_giana_output(giana_outfile)
+}
+
+attach_to_obj = function(obj, out) {
+    out <- as.data.frame(out)
+    rownames(out) <- out$Barcode
+    if (is_seurat) {
+        # Attach results to Seurat object
+        obj@meta.data$CDR3_Cluster <- out[rownames(obj@meta.data), "CDR3_Cluster"]
+    } else {
+        # Attach results to the list of data frames
+        for (sample in names(obj)) {
+            sout <- filter(out, Sample == sample)
+            obj[[sample]]$CDR3_Cluster <- sout[obj[[sample]]$barcode, "CDR3_Cluster"]
+        }
+    }
+    obj
+}
+
+
+if (tolower(tool) == "clustcr") {
+    out = run_clustcr()
+} else if (tolower(tool) == "giana") {
+    out = run_giana()
+} else {
+    stop(paste("Unknown tool:", tool))
+}
+
+log$info("Attaching results to the input object ...")
+out <- attach_to_obj(obj, out)
+
+log$info("Saving results ...")
+save_obj(out, outfile)