Mercurial > repos > artbio > cpm_tpm_rpk
comparison cpm_tpm_rpk.R @ 5:bcff1eb6fdb5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d6ef3d1c1d490967b7b79138573a86a8d5235c43
| author | artbio |
|---|---|
| date | Fri, 06 Oct 2023 18:00:05 +0000 |
| parents | be358a1ebf67 |
| children | f00c1c34565e |
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| 4:be358a1ebf67 | 5:bcff1eb6fdb5 |
|---|---|
| 159 return(tpm) | 159 return(tpm) |
| 160 } | 160 } |
| 161 | 161 |
| 162 #### running code #### | 162 #### running code #### |
| 163 | 163 |
| 164 data <- read.table( | 164 data <- read.delim( |
| 165 opt$data, | 165 opt$data, |
| 166 check.names = FALSE, | 166 check.names = FALSE, |
| 167 header = opt$colnames, | 167 header = opt$colnames, |
| 168 row.names = 1, | 168 row.names = 1, |
| 169 sep = opt$sep | 169 sep = opt$sep |
| 170 ) | 170 ) |
| 171 | 171 |
| 172 if (opt$type == "tpm" || opt$type == "rpk") { | 172 if (opt$type == "tpm" || opt$type == "rpk") { |
| 173 gene_length <- as.data.frame( | 173 gene_length <- as.data.frame( |
| 174 read.table( | 174 read.delim( |
| 175 opt$gene, | 175 opt$gene, |
| 176 header = opt$gene_header, | 176 header = opt$gene_header, |
| 177 row.names = 1, | 177 row.names = 1, |
| 178 sep = opt$gene_sep | 178 sep = opt$gene_sep |
| 179 ) | 179 ) |