Mercurial > repos > iuc > snpfreqplot
annotate helperFunctions.R @ 2:dc51db22310c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
author | iuc |
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date | Fri, 18 Dec 2020 23:48:01 +0000 |
parents | e362b3143cde |
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rev | line source |
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1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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1 #!/usr/bin/env R |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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2 |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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3 ## Helper functions for processing variant data, especially for |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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4 ## data which contains duplicate variants differing only on |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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5 ## annotation. |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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6 |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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7 difference_in_group <- function(lines) { |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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8 #' Find the columns containing the differences between a |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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9 #' group of lines sharing the same POS and ALT. |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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10 #' e.g. |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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11 #' CHROM POS REF ALT IMPACT FUNCLASS AA GENE |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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12 #' 1 NC_045512.2 3037 C T LOW SILENT F924 ORF1ab |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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13 #' 2 NC_045512.2 3037 C T LOW SILENT F106 ORF1ab |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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14 #' 3 NC_045512.2 3037 C T MEDIUM SILENT F106 ORF1ab |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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15 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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16 #' should yield: |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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17 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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18 #' unique.name |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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19 #' 1 3037 T (LOW|F924) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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20 #' 2 3037 T (LOW|F106) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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21 #' 3 3037 T (MEDIUM|F106) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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22 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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23 #' i.e. it identifies that IMPACT and AA are the differing |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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24 #' columns for each of the rows |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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25 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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26 #' Ideally this function should just be used as |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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27 #' ``tab %>% group_by(POS, ALT) %>% difference_in_group()`` |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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28 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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29 diff.colnames <- c() |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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30 nlines <- nrow(lines) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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31 if (nlines > 1) { |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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32 for (i in 1:(nlines - 1)) { |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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33 test1 <- lines[i, ] |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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34 for (j in i:nlines) { |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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35 test2 <- lines[j, ] |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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36 diff.colnames <- c(diff.colnames, |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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37 names(test1[!(test1 %in% test2)])) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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38 } |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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39 } |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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40 } |
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e362b3143cde
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
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41 group_select <- c("POS", "REF", "ALT", diff.colnames) |
e362b3143cde
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
iuc
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42 return(lines[, group_select] %>% unite(group_select, sep = " ")) # nolint |
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1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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43 } |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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44 |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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45 split_table_and_process <- function(tab) { |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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46 #' Split TAB into groups sharing the same POS and ALT |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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47 #' and create distinguishing labels. |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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48 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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49 #' Calls the above ``difference_in_group`` for each |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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50 #' discovered group. |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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51 #' |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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52 #' This function is necessary because tidyr is difficult |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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53 #' to write custom group binding functions. |
1
e362b3143cde
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
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54 group_ind <- tab %>% group_by(POS, REF, ALT) %>% select(POS, REF, ALT) # nolint |
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1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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55 nlines <- nrow(tab) |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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56 groups <- list() |
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dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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57 if (nlines) { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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58 groups[[1]] <- c(1, 1) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
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59 } else { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
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60 groups[[1]] <- c(0, 0) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
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61 } |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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62 if (nlines >= 2) { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
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63 last_pa <- paste(group_ind[1, ]) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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64 for (r in 2:nlines) { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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65 curr_pa <- paste(group_ind[r, ]) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
iuc
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66 group_ind_diff_between_lines <- !all(last_pa == curr_pa) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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67 if (group_ind_diff_between_lines) { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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68 ## end of current group, start of new |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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69 groups[[length(groups)]][2] <- r - 1 ## change prev end |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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70 groups[[length(groups) + 1]] <- c(r, r) ## set (start, end) |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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71 } else if (r == nlines) { |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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72 ## i.e. if the very last line shares |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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73 ## the same POS REF ALT as the one before, |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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74 ## close current group. |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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75 groups[[length(groups)]][2] <- r |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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76 } |
dc51db22310c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
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77 last_pa <- curr_pa |
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1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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78 } |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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79 } |
1062d6ad6503
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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80 as_tibble(do.call( |
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81 "rbind", |
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82 lapply(groups, function(grange) { |
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83 expand_range <- grange[1]:grange[2] |
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84 difference_in_group(tab[expand_range, ]) |
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85 }) |
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86 )) |
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87 } |
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88 |
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89 read_and_process <- function(id) { |
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90 file <- (samples %>% filter(ids == id))$files # nolint |
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91 variants <- read.table(file, header = T, sep = "\t", colClasses = "character") |
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92 variants["AF"] <- lapply(variants["AF"], as.numeric) |
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93 uniq_ids <- split_table_and_process(variants) |
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94 if (nrow(variants) != nrow(uniq_ids)) { |
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95 stop(paste0(id, " '", file, "' failed: ", file, "\"", |
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96 "nrow(variants)=", nrow(variants), |
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97 " but nrow(uniq_ids)=", nrow(uniq_ids))) |
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98 } |
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99 variants <- as_tibble(cbind(variants, uniq_ids)) # nolint |
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100 return(variants) |
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101 } |