Mercurial > repos > greg > create_genome_tracks

comparison create_genome_tracks.R @ 3:3bc9d3e88e7b draft

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author greg
date Fri, 10 Nov 2017 13:50:32 -0500
parents 64b7d66acd75
children 47f6ba0fc3f4
comparison
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2:64b7d66acd75 3:3bc9d3e88e7b
111 system(paste("rm ", paste(outpref, i, "bed1", sep="."))); 111 system(paste("rm ", paste(outpref, i, "bed1", sep=".")));
112 } 112 }
113 return(cells); 113 return(cells);
114 } 114 }
115 115
116 # cell_info: shortid match with those in states,
117 # long id, cell description, text color
118 #run<-function(state_files, hub_id, opt$build, chrom_len_file, state_color, opt$target_url="http://bx.psu.edu/~yuzhang/tmp/", tracks_output_dir=NULL, hub_name=NULL, cell_info=NULL, header=NULL, statename=NULL)
119
120 if(length(opt$hub_name) == 0) { 116 if(length(opt$hub_name) == 0) {
121 hub_name = opt$hub_id; 117 hub_name = opt$hub_id;
122 } 118 }
123 119
124 # Create the tracks output directory. 120 # Create the tracks output directory.
125 if(length(tracks_output_dir) == 0) { 121 tracks_output_dir = paste("tracks_", hub_id, "/", sep="");
126 tracks_output_dir = paste("tracks_", hub_id, "/", sep="");
127 }
128 dir.create(tracks_output_dir, showWarnings=FALSE); 122 dir.create(tracks_output_dir, showWarnings=FALSE);
129 123
130 # Create the color scheme. 124 # Create the color scheme.
131 mc = NULL; 125 mc = NULL;
132 x = read.table(opt$parameter_files, comment="!", nrows=1); 126 x = read.table(opt$parameter_files, comment="!", nrows=1);