add Relatedness calc

tools/Fst_gds/Fst_gds.script.R

@@ -75,7 +75,6 @@ if (popmap_file != '')
 } 
 
 if (nbpops <  2)  { #or no popmap provided
-prin("here")
     # need popmap with at least 2 pops
     write.table(0, file = meanfstFile, append = FALSE, quote = F, sep = '\t', row.names = T, col.names = NA);
     write.table(0, file = fstFile, append = FALSE, quote = F, sep = '\t', row.names = T, col.names = NA);

tools/Relatedness_gds/Relatedness_gds.rule.snakefile

+<step_name>__Relatedness_gds_gds_name = os.path.basename(<step_name>__Relatedness_gds_inputs()["gds"]).split(".")[0]
+
+rule <step_name>__Relatedness_gds:
+    input:
+        **<step_name>__Relatedness_gds_inputs(),
+    output: 
+        k0 = config["results_dir"] + "/" + config["<step_name>__Relatedness_gds_output_dir"] + "/" + <step_name>__Relatedness_gds_gds_name + "_k0.txt",
+        k1 = config["results_dir"] + "/" + config["<step_name>__Relatedness_gds_output_dir"] + "/" + <step_name>__Relatedness_gds_gds_name + "_k1.txt",
+        k0vsk1_png = config["results_dir"] + "/" + config["<step_name>__Relatedness_gds_output_dir"] + "/K0vsK1_plot_mqc.png",
+        k1_heatmap_png = config["results_dir"] + "/" + config["<step_name>__Relatedness_gds_output_dir"] + "/K1_heatmap_mqc.png",
+    params: 
+        method = config["<step_name>__Relatedness_gds_method"],
+        output_dir = config["results_dir"] + "/" + config["<step_name>__Relatedness_gds_output_dir"]+ "/",
+        command = config["<step_name>__Relatedness_gds_command"],
+    threads:
+            config["<step_name>__Relatedness_gds_threads"]           
+    log: 
+        config["results_dir"] + "/logs/" + config["<step_name>__Relatedness_gds_output_dir"] + "/Relatedness_gds_log.txt"
+    script:
+        config["<step_name>__Relatedness_gds_script"]    
+    

tools/Relatedness_gds/Relatedness_gds.script.R

+library(SNPRelate);
+library(SeqArray);
+
+
+#popmap_file = snakemake@input[["popmap_file"]]
+gdsFile = snakemake@input[["gds"]]
+
+k0vsk1_png = snakemake@output[["k0vsk1_png"]]
+K1_heatmap_png = snakemake@output[["K1_heatmap_png"]]
+
+k0File = snakemake@output[["k0"]]
+k1File = snakemake@output[["k1"]]
+
+methode = snakemake@params[["method"]]
+threads = snakemake@threads
+
+gds = seqOpen(gdsFile);
+
+switch(methode, 
+MoM={
+  # PLINK method of moment
+  pibd <- snpgdsIBDMoM(gds,autosome.only=FALSE,num.thread=threads )
+},
+EM={
+     #by Maximum Likelihood Estimation.  EM  algorithm of searching maximum value of log likelihood function
+  pibd <- snpgdsIBDMLE(gds, method = "EM", autosome.only=FALSE,num.thread=threads)
+   
+},
+downhill.simplex = {
+    #by Maximum Likelihood Estimation.  downhill.simplex  algorithm of searching maximum value of log likelihood function
+   pibd <- snpgdsIBDMLE(gds, method = "downhill.simplex", autosome.only=FALSE,num.thread=threads )
+
+}
+)
+
+
+
+flag <- lower.tri(pibd$k0)
+png(file=k0vsk1_png, width=1024, height=1024); 
+    plot(NaN, xlim=c(0,1), ylim=c(0,1), xlab="k0", ylab="k1")
+    lines(c(0,1), c(1,0), col="red", lty=3)
+    points(pibd$k0[flag], pibd$k1[flag])
+dev.off()
+
+rownames(pibd$k0) = pibd$sample.id ; colnames(pibd$k0) = pibd$sample.id
+rownames(pibd$k1) = pibd$sample.id ; colnames(pibd$k0) = pibd$sample.id
+
+png(file=K1_heatmap_png, width=1024, height=1024); 
+   heatmap(pibd$k1) ; 
+dev.off()
+
+write.table(pibd$k0, file = k0File, append = FALSE, quote = F, sep = '\t', row.names = T, col.names = NA);
+
+write.table(pibd$k1, file = k1File, append = FALSE, quote = F, sep = '\t', row.names = T, col.names = NA);
+seqClose(gds);
+

tools/Relatedness_gds/Relatedness_gds.yaml

+{
+  id: Relatedness_gds,
+  name: identity-by-descent IBD,
+  article: "",
+  website: "",
+  git: "",
+  description: "identity-by-descent (IBD) estimation in SNPRelate either with the method of moments (MoM) (Purcell et al., 2007) or maximum likelihood estimation (MLE) (Milligan, 2003; Choi et al., 2009)",
+  version: "",
+  documentation: "",
+  multiqc: "custom",
+  commands:
+    [
+      {
+        name: Relatedness_gds,
+        command: "",
+        category: "genet_pop",
+        output_dir: Relatedness_gds,
+        inputs: [{ name: gds, type: "gds", file: "",description: "gds file"} ,
+                ],
+        outputs: [
+          { name: k0, type: "txt", file: "*_k0.txt", description: "IBD coefficient, the probability of sharing ZERO IBD" },
+          { name: k1, type: "txt", file: "*_k1.txt", description: "IBD coefficient, the probability of sharing ONE IBD" },
+          { name: k0vsk1_png, type: "png", file: "K0vsK1_plot_mqc.png", description: "K0 vs K1 plot" },
+          { name: K1_heatmap_png, type: "png", file: "K1_heatmap_mqc.png", description: "A heatmap of K1 values" },
+
+          
+        ],
+        options: [
+          {
+              name: "Relatedness_gds_method",
+              type: "radio",
+              value: "MoM",
+              choices: [Plink Method of Moment: MoM, ML using EM algo: EM, ML using downhill.simplex algo: downhill.simplex],
+              label: "Method to calculate IBD coef.",
+          },
+          {
+              name: "Relatedness_gds_threads",
+              prefix: "--threads",
+              value: 16,
+              min: 1,
+              max: 64,
+              step: 1,
+              label: "Threads to use",
+              type: "numeric",
+          },
+        ],
+      },
+    ],
+  script: Relatedness_gds.script.R,
+  install:
+    {
+      SNPRelate: [
+        'Rscript -e ''if (!requireNamespace("BiocManager", quietly = TRUE))  install.packages("BiocManager");
+         BiocManager::install("SNPRelate", update = TRUE, ask = FALSE)'' '
+      ],
+      SeqArray: [
+        'Rscript -e ''if (!requireNamespace("BiocManager", quietly = TRUE))  install.packages("BiocManager");
+         BiocManager::install("SeqArray", update = TRUE, ask = FALSE)'' '
+      ], 
+    },
+  citations:
+    {
+     SNPRelate: [
+       "Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics, 28(24), 3326-3328. doi: 10.1093/bioinformatics/bts606. " 
+       ],
+     SeqArray: [
+       "Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir B, Laurie C, Levine D (2017). SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi: 10.1093/bioinformatics/btx145." 
+       ],  
+     PLINK: [
+       "Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81."
+     ] 
+    },
+}