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comparison hairpinTool.R @ 4:f8af57d6f60b

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Fixed bug causing fastq input to break - Moved misplaced error check causing fastq inputs to not function
author shian_su <registertonysu@gmail.com>
date Mon, 24 Feb 2014 14:41:39 +1100
parents 076ca575208f
children 3d04308a99f9
comparison
equal deleted inserted replaced
2:076ca575208f 4:f8af57d6f60b
168 offenders <- unmake.names(offenders) 168 offenders <- unmake.names(offenders)
169 stop("ID column of sample annotation must have unique values, values ", 169 stop("ID column of sample annotation must have unique values, values ",
170 offenders, " are repeated") 170 offenders, " are repeated")
171 } # Check that IDs in sample annotation are unique 171 } # Check that IDs in sample annotation are unique
172 172
173 if (any(is.na(match(samples$ID, colnames(counts))))) {
174 stop("not all samples have groups specified")
175 } # Check that a group has be specifed for each sample
176
177 if (inputType=="fastq") { 173 if (inputType=="fastq") {
178 174
179 if (any(table(hairpins$ID)>1)){ 175 if (any(table(hairpins$ID)>1)){
180 tab <- table(hairpins$ID) 176 tab <- table(hairpins$ID)
181 offenders <- paste(names(tab[tab>1]), collapse=", ") 177 offenders <- paste(names(tab[tab>1]), collapse=", ")
182 stop("ID column of hairpin annotation must have unique values, values ", 178 stop("ID column of hairpin annotation must have unique values, values ",
183 offenders, " are repeated") 179 offenders, " are repeated")
184 } # Check that IDs in hairpin annotation are unique 180 } # Check that IDs in hairpin annotation are unique
185 181
186 } else if (inputType=="counts") { 182 } else if (inputType=="counts") {
183 if (any(is.na(match(samples$ID, colnames(counts))))) {
184 stop("not all samples have groups specified")
185 } # Check that a group has be specifed for each sample
187 186
188 if (any(table(counts$ID)>1)){ 187 if (any(table(counts$ID)>1)){
189 tab <- table(counts$ID) 188 tab <- table(counts$ID)
190 offenders <- paste(names(tab[tab>1]), collapse=", ") 189 offenders <- paste(names(tab[tab>1]), collapse=", ")
191 stop("ID column of count table must have unique values, values ", 190 stop("ID column of count table must have unique values, values ",
291 hpReadout <- gsub(" -- ", "", hpReadout, fixed=TRUE) 290 hpReadout <- gsub(" -- ", "", hpReadout, fixed=TRUE)
292 291
293 292
294 # Make the names of groups syntactically valid (replace spaces with periods) 293 # Make the names of groups syntactically valid (replace spaces with periods)
295 data$samples$group <- make.names(data$samples$group) 294 data$samples$group <- make.names(data$samples$group)
296 } else { 295 } else if (inputType=="counts") {
297 # Process counts information, set ID column to be row names 296 # Process counts information, set ID column to be row names
298 rownames(counts) <- counts$ID 297 rownames(counts) <- counts$ID
299 counts <- counts[ , !(colnames(counts)=="ID")] 298 counts <- counts[ , !(colnames(counts)=="ID")]
300 countsRows <- nrow(counts) 299 countsRows <- nrow(counts)
301 300