Estimation motifs

bin/2.2_motif_estimation/png_to_pdf.R

@@ -39,16 +39,16 @@ png_to_pdf <- function(png_top, png_list, cluster_ids, new_id, out = "cluster.pd
   grobs <- lapply(png_split,function(p){rasterGrob(readPNG(p),interpolate = FALSE)})
 
   split_grobs <- split(grobs, rep(1:ceiling(length(grobs)/3), each = 3)[1:length(grobs)])
-  
+
   rows <- lapply(seq(1,length(split_grobs)), function(sg){
     arrangeGrob(grobs = split_grobs[[sg]], top = textGrob(paste0("Cluster ",cluster_list[sg]),gp = gpar(fontsize = 20,font = 3)), ncol = 3)
   })
   split_rows <- split(rows, rep(1:ceiling(length(rows)/4), each = 4)[1:length(rows)])
-  
+
   pdf(out,width = 17, height = 11)
   grid.arrange(grobs = top_grob, nrow = 3, top = textGrob(paste0("New Cluster ",new_id),gp = gpar(fontsize = 30,font = 3)))
   lapply(split_rows, function(r){
-    grid.arrange(grobs = r, nrow = 4, top = textGrob("Generated from...",gp = gpar(fontsize = 30,font = 3))) 
+    grid.arrange(grobs = r, nrow = 4, top = textGrob("Generated from...",gp = gpar(fontsize = 30,font = 3)))
   })
 
   dev.off()
@@ -68,27 +68,25 @@ get_index <- function(index_file){
   index <- f[,c(2,8)]
   index$V8 <- strsplit(index$V8,",")
   return(index[unlist(lapply(index$V8, function(v){ifelse(length(v) > 1, TRUE, FALSE)}))])
-
-}
 
+}
 
+@TODO
 png_to_pdf_set_up <- function(png_top, png_list, index_file){
-  
+
   index <- get_index(index_file)
   t <- lapply(seq(nrow(index)), function(i){
     new_id <- index[i,1]
     cluster_ids <- index[i,2]
     out <- paste0("Summary_cluster_", new_id, ".pdf")
-    png_to_pdf(png_top = ,png_list = ,cluster_ids = cluster_ids, new_id = new_id, out = out )
+    #regex_png <- paste0("*_cluster_", new_id , "/logo${NUM}.png") #????
+    png_to_pdf(png_top = "TODO" ,png_list = "TODO" ,cluster_ids = cluster_ids, new_id = new_id, out = out )
   })
-  
+
 }
 
 
 # run function merge_similar with given parameteres if not in interactive context (e.g. run from shell)
 if (!interactive()) {
   png_to_pdf_set_up(opt$png_new, opt$png_old , opt$index)
 }
-
-
-

pipeline.nf

@@ -68,9 +68,51 @@ disable_mo_clu = 1
 //evaluation
 	params.max_uropa_runs = 10
 
-if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || (params.gtf_annotation == "" && params.gtf_merged == "" ) || "${params.help}" != "0" ) {
-	log.info """
-	Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
+/*
+Checking for parameter input!
+*/
+int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer",
+             "aprox_motif_len", "motif_occurrence", "min_seq_length", "global",
+             "sequence_coverage", "memory", "throw_away_seq", "strand",
+             "min_seq", "motif_min_key", "motif_max_key", "iteration",
+             "edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight",
+						 "threads", "max_uropa_runs"]
+file_params = ["bigwig", "bed", "genome_fasta", "motif_db", "config", "gtf_annotation",]
+all_params = int_params + file_params + ["organism" , "identity", "tfbsscan_method",
+							"percentage", "tomtom_treshold", "motif_similarity_thresh", "out",
+							"tissues", "gtf_merged", "cluster_motif", "tfbs_path", "help", "seed"]
+req_params = file_params + ["organism"]
+
+valid_organism = ["hg38", "hg19", "mm9", "mm10"]
+valid_tfbsscan_methods = ["moods","fimo"]
+val_missing = false
+send_help = false
+missing_params = []
+
+req_params.each { key ->
+	if (req_params.contains(key)){
+		if (key == "gtf_annotation") {
+			if (params[key] == "" && params.gtf_merged == "") {
+				val_missing = true
+				missing_params.add("$key or gtf_merged")
+			}
+		} else {
+			if (params[key] == ""){
+				val_missing = true
+				missing_params.add(key)
+			}
+		}
+	}
+}
+
+if (val_missing){
+	send_help = true
+	println("Error: Following required parameters are missing: $missing_params")
+}
+
+if (send_help || "${params.help}" != "0") {
+log.info """
+Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
 
 	Required arguments:
 		--bigwig		 Path to BigWig-file
@@ -79,7 +121,7 @@ if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.g
 		--motif_db		 Path to motif-database in MEME-format
 		--config		 Path to UROPA configuration file
 		--gtf_annotation	Path to gtf annotation file
-	 	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
+		--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
 		--out			 Output Directory (Default: './out/')
 
 	Optional arguments:
@@ -132,9 +174,8 @@ if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.g
 					config
 		Evaluation:
 		--max_uropa_runs INT	 Maximum number UROPA runs running parallelized (Default: 10)
-	All arguments can be set in the configuration files
-	 ```
-	"""
+All arguments can be set in the configuration files
+"""
 	System.exit(2)
 } else {
 	Channel.fromPath(params.bigwig).map {it -> [it.simpleName, it]}.set {bigwig_input}
@@ -150,25 +191,6 @@ if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.g
 	}
 }
 
-
-
-/*
-Checking for parameter input!
-*/
-int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer",
-             "aprox_motif_len", "motif_occurrence", "min_seq_length", "global",
-             "sequence_coverage", "memory", "throw_away_seq", "strand",
-             "min_seq", "motif_min_key", "motif_max_key", "iteration",
-             "edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight",
-						 "threads", "max_uropa_runs"]
-req_params = ["bigwig", "bed", "genome_fasta", "motif_db", "config"]
-all_params = int_params + req_params + ["organism" , "identity", "tfbsscan_method",
-							"percentage", "tomtom_treshold", "motif_similarity_thresh", "out",
-							"tissues", "gtf_merged", "cluster_motif", "tfbs_path", "help", "gtf_annotation", "seed"]
-
-valid_organism = ["hg38", "hg19", "mm9", "mm10"]
-valid_tfbsscan_methods = ["moods","fimo"]
-
 params.each { key, value ->
 	if (!(all_params.contains(key))){
 		println("Warning: Parameter $key is unknown. Please check for typos or the parameter list!")
@@ -179,13 +201,14 @@ params.each { key, value ->
       System.exit(2)
     }
   }
-  if(req_params.contains(key) || (key == "gtf_merged" && value != "") ) {
+  if(file_params.contains(key) || (key == "gtf_merged" && value != "") ) {
     if(!file(value).exists()) {
       println("ERROR: $key not found. Please check the given path.")
       System.exit(2)
     }
   }
 }
+
 if (!("${params.identity}" ==~ /^0\.[8-9][[0-9]*]?|^1(\.0)?/ )){
   println("ERROR: --identity needs to be float in range 0.8 to 1.0")
   System.exit(2)