From 50fb433424cc63f14539cca2d46fd37f1f7fee8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Sat, 15 Dec 2018 17:14:31 -0500 Subject: [PATCH] documentation --- bin/bed_to_fasta.R | 6 +++--- bin/motif_estimation.nf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/bed_to_fasta.R b/bin/bed_to_fasta.R index 6cefe43..84910f3 100644 --- a/bin/bed_to_fasta.R +++ b/bin/bed_to_fasta.R @@ -14,14 +14,14 @@ min_seq <- args[3] bed <- data.table::fread(bedInput, header = FALSE, sep = "\t") -clusters <- split(bed, bed$V11, sorted = TRUE, flatten = FALSE) # <---- Spalte mit Cluster +clusters <- split(bed, bed$V11, sorted = TRUE, flatten = FALSE) # <---- Cluster column discard <- lapply(1:length(clusters), function(i){ clust <- as.data.frame(clusters[i]) print(nrow(clust)) if (nrow(clust) >= as.numeric(min_seq) ) { - sequences <- as.list(clust[[10]]) # <---- Splate mit Sequenz + sequences <- as.list(clust[[10]]) # <---- sequenze column outfile <- paste0(prefix,"_cluster_",i,".FASTA") - seqinr::write.fasta(sequences = sequences, names = clust[[4]], file.out = outfile, as.string = TRUE) # <---- Spalte mit Name + seqinr::write.fasta(sequences = sequences, names = clust[[4]], file.out = outfile, as.string = TRUE) # <---- Name column } else { print(paste0("Cluster: ",i," is to small")) } diff --git a/bin/motif_estimation.nf b/bin/motif_estimation.nf index f5b96e3..430040e 100644 --- a/bin/motif_estimation.nf +++ b/bin/motif_estimation.nf @@ -24,7 +24,7 @@ motif_similarity_thresh = 0.00001 // threshold for motif similarity score if (params.bed == "" || params.out == "" || params.motif_db == "" || params.path_env || "${params.help}" == "1") { log.info """ -Usage: nextflow run pipeline.nf --bed [PATH] --out [PATH] --motif_db [PATH] --path_env YAML-file +Usage: nextflow run motif_estimation.nf --bed [PATH] --out [PATH] --motif_db [PATH] --path_env YAML-file --bed Path Input BED-file (Column with cluster: 11; column with sequenze: 10)!! --out Path Output Path --motif_db Path Path to MEME-Database