Mercurial > repos > greg > ideas_genome_tracks
changeset 15:f8c479d219bd draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 16 Nov 2017 14:36:47 -0500 |
| parents | 99c9770fdd7f |
| children | be53d516a8ef |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Thu Nov 16 13:41:12 2017 -0500 +++ b/ideas_genome_tracks.R Thu Nov 16 14:36:47 2017 -0500 @@ -122,7 +122,7 @@ track_file_name_bigbed <- paste(base_track_file_name, i, "bigbed", sep=".") write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F); system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed)); - #system(paste("rm ", track_file_name_bed)); + system(paste("rm ", track_file_name_bed)); } return(cells); } @@ -171,13 +171,13 @@ track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, opt$header, tracks_dir, opt$hub_id, hub_name, state_color, opt$state_name, opt$cell_info); # Write the outputs. -track_db_file_path <- paste(tracks_dir, "/", paste("trackDb_", opt$hub_id, ".txt", sep=""), sep="") +track_db_file_path <- paste(tracks_dir, "/", paste("trackDb.txt", sep=""), sep="") write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F); -obj_name <- c(paste("genome", opt$build), paste("trackDb trackDb_", opt$hub_id, ".txt", sep="")) -genomes_file_path <- paste(opt$output_hub_files_path, "/", "genomes_", opt$hub_id, ".txt", sep="") -write.table(obj_name, file=genomes_file_path, quote=F, row.names=F, col.names=F); +contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep="")) +genomes_file_path <- paste(opt$output_trackhub_files_path, "/", "genomes.txt", sep="") +write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F); -obj_name <- c(paste("hub", opt$hub_id), paste("shortLabel", opt$hub_id), paste("longLabel", hub_name), paste("genomesFile genomes_", opt$hub_id, ".txt", sep=""), paste("email", opt$email)) -hub_file_path <- paste(opt$output_hub_files_path, "/", "hub_", opt$hub_id, ".txt", sep="") -write.table(obj_name, file=hub_file_path, quote=F, row.names=F, col.names=F); +contents <- c(paste("hub", opt$hub_id), paste("shortLabel", opt$hub_id), paste("longLabel", hub_name), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email)) +hub_file_path <- paste(opt$output_trackhub_files_path, "/", "hub.txt", sep="") +write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);