Commit eda59ee5 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

release v8.4.0: Same bug fixed elsewhere

parent d4960087
......@@ -209,6 +209,11 @@ Gitlab developers
## WHAT'S NEW IN
### v8.4.0
1) Same bug fixed elsewhere
### v8.3.0
1) Small bug removed: now same orientation plotted in the CDS plots
......
......@@ -482,15 +482,25 @@ if(tss_path != "NULL"){
names(obs.rd.freq)[names(obs.rd.freq) == "Sequence"] <- "KIND"
obs.rd.freq$KIND <- toupper(obs.rd.freq$KIND)
obs.rd.freq$orient <- toupper(obs.rd.freq$orient)
names(obs.rd.pos)[names(obs.rd.pos) == "Sequence"] <- "KIND"
obs.rd.pos$KIND <- toupper(obs.rd.pos$KIND)
obs.rd.pos$orient <- toupper(obs.rd.pos$orient)
obs.pos <- obs.rd.pos[obs.rd.pos$KIND == "OBS", ]
tss$orient <- toupper(tss$orient)
cds[ , 6] <- toupper(cds[ , 6] )
tempo <- max(obs.rd.freq$freq) + 20
ori.freq <- data.frame(x= c(ori_coord[1], ori_coord[1], ori_coord[2], ori_coord[2], ori_coord[1]), y = c(-tempo, tempo, tempo, -tempo ,-tempo), ZONE = "Ori", stringsAsFactors = TRUE)
dif.freq <- data.frame(x= c(ter_coord[1], ter_coord[1], ter_coord[2], ter_coord[2], ter_coord[1]), y = c(-tempo, tempo, tempo, -tempo ,-tempo), ZONE = "Ter", stringsAsFactors = TRUE)
structure.freq <- rbind(ori.freq, dif.freq, stringsAsFactors = TRUE)
obs.freq <- obs.rd.freq[obs.rd.freq$KIND == "obs", ]
obs.freq <- obs.rd.freq[obs.rd.freq$KIND == "OBS", ]
names(obs.rd.pos)[names(obs.rd.pos) == "Sequence"] <- "KIND"
obs.pos <- obs.rd.pos[obs.rd.pos$KIND == "obs", ]
############ end modifications of imported tables
......@@ -571,7 +581,7 @@ if(ncol(obs.freq) > 0){
invisible(dev.off())
png(filename = paste0("plot_", file_name, "_insertion_hist_forward.png"), width = 5000, height = 1800, units = "px", res = 300)
tempo1 <- table(obs.freq$freq[obs.freq$orient == "Forward"])
tempo1 <- table(obs.freq$freq[obs.freq$orient == "FORWARD"])
tempo2 <- names(tempo1)
names(tempo1) <- NULL
tempo3 <- data.frame(insertion_number = as.integer(tempo2), site_number = as.vector(tempo1))
......@@ -605,7 +615,7 @@ if(ncol(obs.freq) > 0){
invisible(dev.off())
png(filename = paste0("plot_", file_name, "_insertion_hist_reverse.png"), width = 5000, height = 1800, units = "px", res = 300)
tempo1 <- table(obs.freq$freq[obs.freq$orient == "Reverse"])
tempo1 <- table(obs.freq$freq[obs.freq$orient == "REVERSE"])
tempo2 <- names(tempo1)
names(tempo1) <- NULL
tempo3 <- data.frame(insertion_number = as.integer(tempo2), site_number = as.vector(tempo1))
......@@ -643,7 +653,7 @@ invisible(dev.off())
png(filename = paste0("plot_", file_name, "_insertion_raw.png"), width = 5000, height = 1800, units = "px", res = 300)
if(ncol(obs.rd.freq) > 0){
tempo <- obs.rd.freq
tempo$freq[tempo$orient == "Reverse"] <- tempo$freq[tempo$orient == "Reverse"] * -1
tempo$freq[tempo$orient == "REVERSE"] <- tempo$freq[tempo$orient == "REVERSE"] * -1
fun_gg_scatter(
data1 = list(structure.freq, tempo), # res # res[res$KIND == "obs", ]
x = list("x", "Position"),
......@@ -673,10 +683,10 @@ invisible(dev.off())
for(i0 in window_size){
# leading and lagging
lead.obs <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Leading" & obs.rd.pos$KIND == "obs"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lag.obs <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Lagging" & obs.rd.pos$KIND == "obs"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lead.rd <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Leading" & obs.rd.pos$KIND == "random"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lag.rd <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Lagging" & obs.rd.pos$KIND == "random"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lead.obs <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Leading" & obs.rd.pos$KIND == "OBS"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lag.obs <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Lagging" & obs.rd.pos$KIND == "OBS"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lead.rd <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Leading" & obs.rd.pos$KIND == "RANDOM"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lag.rd <- fun_slide(data = obs.rd.pos$Position[obs.rd.pos$fork== "Lagging" & obs.rd.pos$KIND == "RANDOM"], window.size = i0, step = step, fun = length, from = min(obs.rd.pos$Position), to = max(obs.rd.pos$Position), parall = TRUE, thread.nb = task.cpus, cute.path = cute)
lead.obs <- data.frame(lead.obs, STRAND = "Leading", KIND = "OBS", stringsAsFactors = TRUE)
......@@ -941,8 +951,8 @@ if(tss_path != "NULL"){
fun_report(data = paste0("\n\nERROR: nrow(final) DIFFERENT FROM nrow(obs.rd.pos)\n\n"), output = log, path = "./", overwrite = FALSE)
}else{
names(final)[names(final) == "seq"] <- "KIND"
final$KIND[final$KIND == "obs"] <- "OBS"
final$KIND[final$KIND == "random"] <- "RANDOM"
# final$KIND[final$KIND == "OBS"] <- "OBS"
# final$KIND[final$KIND == "RANDOM"] <- "RANDOM"
options(scipen = 1000) # to avoid writing of scientific numbers in tables, see https://stackoverflow.com/questions/3978266/number-format-writing-1e-5-instead-of-0-00001
tempo.cat <- paste0("TABLE SAVED IN: ", paste0("./distance.insertion.tss.txt"))
fun_report(data = paste0("\n ", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
......@@ -1355,7 +1365,7 @@ if(tss_path != "NULL"){
fun_report(data = paste0("\n\nCHECK ON THE OBSERVED DATA ONLY:\n\n"), output = log, path = "./", overwrite = FALSE)
obs <- inside.gene[inside.gene$KIND == "obs", ]
obs <- inside.gene[inside.gene$KIND == "OBS", ]
fun_report(data = paste0("\n\nNUMBER OF ROWS FOR obs[obs$cds.nb == 1, ]: ", nrow(obs[obs$cds.nb == 1, ])), output = log, path = "./", overwrite = FALSE)
fun_report(data = paste0("\n\nNUMBER OF ROWS FOR nrow(obs[obs$cds.nb == 1, ]) + nrow(outside.gene): ", nrow(obs[obs$cds.nb == 1, ]) + nrow(outside.gene)), output = log, path = "./", overwrite = FALSE)
......@@ -1389,8 +1399,8 @@ if(tss_path != "NULL"){
res$essential[res$essential == "FALSE"] <- "DISPENSABLE"
res <- as.data.frame(res, stringsAsFactors = TRUE)
names(res)[names(res) == "KIND"] <- "KIND"
res$KIND[res$KIND == "obs"] <- "OBS"
res$KIND[res$KIND == "random"] <- "RANDOM"
# res$KIND[res$KIND == "obs"] <- "OBS"
# res$KIND[res$KIND == "random"] <- "RANDOM"
fun_report(data = paste0("\n\nres (inside.gene.pos_prop.txt) FILE HEAD:"), output = log, path = "./", overwrite = FALSE)
fun_report(data = head(res), output = log, path = "./", overwrite = FALSE)
fun_report(data = paste0("\n\nres (inside.gene.pos_prop.txt) INFO:"), output = log, path = "./", overwrite = FALSE)
......@@ -1447,7 +1457,7 @@ if(tss_path != "NULL"){
for(i0 in 1:length(files)){
assign(files[i0], read.table(paste0("./", files[i0], ".txt"), sep = "\t", stringsAsFactors = FALSE, header = TRUE))
assign(files[i0], data.frame(get(files[i0]), site = site[i0], stringsAsFactors = FALSE))
assign(files[i0], {x <- get(files[i0]); names(x)[names(x) == "KIND"] <- "type" ; x$type[x$type == "obs"] <- "OBS" ; x$type[x$type == "random"] <- "RANDOM" ; x})
assign(files[i0], {x <- get(files[i0]); names(x)[names(x) == "KIND"] <- "type" ; x$type[x$type == "OBS"] <- "OBS" ; x$type[x$type == "RANDOM"] <- "RANDOM" ; x})
}
inside.gene.pos_prop$same_orient[inside.gene.pos_prop$same_orient == TRUE] <- "SAME"
......
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
1 bc/621cf6 13881 init COMPLETED 0 2022-04-08 17:04:01.731 1.5s 21ms 5.8% 0 0 104.1 KB 665 B
3 23/20fe6a 13943 report1 COMPLETED 0 2022-04-08 17:04:01.810 1.6s 18ms 5.6% 0 0 104.4 KB 683 B
5 2e/15e09d 14029 backup COMPLETED 0 2022-04-08 17:04:02.010 1.5s 12ms 5.3% 0 0 104.3 KB 500 B
2 f6/cbcfc5 13907 Nremove (1) COMPLETED 0 2022-04-08 17:04:01.773 1.9s 449ms 49.5% 11.9 MB 70.6 MB 16.8 MB 14.5 MB
6 76/bdb5e7 14055 workflowVersion COMPLETED 0 2022-04-08 17:04:02.037 2.1s 830ms 11.9% 5 MB 38.4 MB 133.5 KB 2.1 KB
7 f3/ab119d 14829 trim (1) COMPLETED 0 2022-04-08 17:04:03.749 2.9s 1.9s 46.9% 42.2 MB 5.6 GB 16.4 MB 12 MB
9 1a/2001d0 15389 kraken (1) COMPLETED 0 2022-04-08 17:04:06.637 89ms 13ms 50.0% 0 0 150.8 KB 220 B
10 01/5957b3 15428 fivep_filtering (1) COMPLETED 0 2022-04-08 17:04:06.669 2.8s 1.8s 26.7% 9.8 MB 61.4 MB 28 MB 15.3 MB
11 8c/a57caf 16229 cutoff (1) COMPLETED 0 2022-04-08 17:04:09.529 1.7s 671ms 19.6% 9.7 MB 61.3 MB 7 MB 3.9 MB
8 e7/1d5b78 15499 fastqc1 (1) COMPLETED 0 2022-04-08 17:04:06.696 5.8s 4.9s 79.7% 178 MB 3.1 GB 13.9 MB 1.2 MB
12 c7/4b7f1a 16203 fastqc2 (1) COMPLETED 0 2022-04-08 17:04:09.504 5.9s 5s 76.8% 167.7 MB 3.1 GB 12.2 MB 1.2 MB
15 39/8acdc1 17088 bowtie2 (1) COMPLETED 0 2022-04-08 17:04:12.272 4.7s 3.6s 56.8% 114.6 MB 239.5 MB 35 MB 16.2 MB
4 46/df156c 14167 motif COMPLETED 0 2022-04-08 17:04:02.369 15.8s 14.7s 51.3% 191.8 MB 317.8 MB 47.6 MB 39.7 MB
16 63/da64fb 17954 Q20 (1) COMPLETED 0 2022-04-08 17:04:17.955 1.5s 341ms 22.8% 6.5 MB 43.3 MB 3.2 MB 2.2 MB
19 48/831122 18538 no_soft_clipping (1) COMPLETED 0 2022-04-08 17:04:20.453 1.4s 294ms 13.0% 3.5 MB 38.4 MB 2.1 MB 1.5 MB
20 c7/51bcb2 18552 duplicate_removal (1) COMPLETED 0 2022-04-08 17:04:20.475 2.9s 1.9s 24.9% 7.4 MB 53 MB 12.9 MB 6.6 MB
18 cf/8b09ae 17980 multiQC COMPLETED 0 2022-04-08 17:04:17.974 7.8s 7s 45.1% 70.3 MB 80.5 MB 28.3 MB 2.3 MB
23 d3/09cb38 19624 insertion (1) COMPLETED 0 2022-04-08 17:04:24.406 1.5s 496ms 20.7% 9.1 MB 65.6 MB 2.5 MB 1.7 MB
24 53/90dda7 19634 insertion (2) COMPLETED 0 2022-04-08 17:04:24.425 1.6s 544ms 21.9% 9 MB 65.7 MB 3 MB 2.2 MB
13 5d/24658b 18078 plot_fivep_filtering_stat (1) COMPLETED 0 2022-04-08 17:04:18.185 12.2s 11.3s 57.3% 210.4 MB 346.8 MB 18.2 MB 792.5 KB
14 0a/948f67 20381 plot_read_length (1) COMPLETED 0 2022-04-08 17:04:30.425 12.4s 11.7s 64.2% 277.1 MB 413.2 MB 18.7 MB 691.5 KB
17 bd/abfcc9 21090 coverage (1) COMPLETED 0 2022-04-08 17:04:42.814 1.5s 605ms 20.4% 5 MB 44.6 MB 479.6 KB 91 KB
21 af/2e0e6e 21249 coverage (2) COMPLETED 0 2022-04-08 17:04:44.274 1.4s 571ms 20.0% 5 MB 44.6 MB 335 KB 82.4 KB
22 f0/f539e8 21406 coverage (3) COMPLETED 0 2022-04-08 17:04:45.694 1.4s 572ms 19.9% 5 MB 44.6 MB 310.2 KB 82.1 KB
25 d5/e7cf5d 21561 final_insertion_files (1) COMPLETED 0 2022-04-08 17:04:47.103 5.4s 4.6s 45.4% 121.7 MB 247 MB 17.2 MB 269.2 KB
31 41/db000b 21973 report3 (1) COMPLETED 0 2022-04-08 17:04:52.546 961ms 29ms 13.0% 0 0 176.8 KB 525 B
26 e5/c4c793 21945 final_insertion_files (2) COMPLETED 0 2022-04-08 17:04:52.515 5.4s 4.6s 45.0% 122.5 MB 247.5 MB 17.2 MB 278.8 KB
27 59/1608f7 22459 plot_coverage (1) COMPLETED 0 2022-04-08 17:04:57.934 11s 10.3s 60.4% 218.3 MB 355.3 MB 18.3 MB 440.1 KB
28 46/fee702 23123 plot_coverage (2) COMPLETED 0 2022-04-08 17:05:08.984 11s 10.2s 60.4% 219.6 MB 355.3 MB 18.3 MB 434.3 KB
29 ef/14b96e 23776 plot_coverage (3) COMPLETED 0 2022-04-08 17:05:19.945 11s 10.2s 60.9% 219.3 MB 355.4 MB 18.3 MB 434.9 KB
32 57/6f5a3a 24429 random_insertion (1) COMPLETED 0 2022-04-08 17:05:30.924 9.1s 8.4s 56.8% 351.6 MB 487.6 MB 30 MB 1.2 MB
30 7a/c33509 24970 seq_around_insertion (1) COMPLETED 0 2022-04-08 17:05:39.994 5.3s 4.6s 45.1% 121.5 MB 246.8 MB 17.2 MB 208.4 KB
33 27/842619 25363 seq_around_insertion (2) COMPLETED 0 2022-04-08 17:05:45.326 5.5s 4.8s 44.6% 121.4 MB 246.8 MB 17.2 MB 229.8 KB
34 e8/d173b9 25743 dup_insertion_and_logo (1) COMPLETED 0 2022-04-08 17:05:50.817 11.6s 10.8s 63.2% 235.4 MB 371.9 MB 16.6 MB 506.4 KB
35 fb/0fb02c 26472 plot_insertion (1) COMPLETED 0 2022-04-08 17:06:02.405 4m 1s 4m 36.1% 400.5 MB 553.2 MB 44.8 MB 22.3 MB
36 83/0441f4 32766 extract_seq (1) COMPLETED 0 2022-04-08 17:10:03.165 1.8s 880ms 18.3% 5.9 MB 50.2 MB 9.1 MB 4.5 MB
38 41/2a7305 551 base_freq (1) COMPLETED 0 2022-04-08 17:10:05.028 1.3s 84ms 10.0% 0 0 279.7 KB 16.8 KB
39 8d/ae6905 585 base_freq (2) COMPLETED 0 2022-04-08 17:10:05.046 1.5s 100ms 9.0% 0 0 281.8 KB 18.9 KB
41 59/5d017c 619 base_freq (4) COMPLETED 0 2022-04-08 17:10:05.066 1.6s 94ms 13.6% 0 0 281.9 KB 19 KB
40 70/896d76 667 base_freq (3) COMPLETED 0 2022-04-08 17:10:05.089 1.6s 93ms 11.4% 0 0 282.6 KB 19.7 KB
37 80/3a0d0a 512 extract_seq (2) COMPLETED 0 2022-04-08 17:10:04.967 2.3s 1.2s 16.0% 5.8 MB 50.2 MB 9.1 MB 4.6 MB
47 1e/dc05b1 1242 base_freq (5) COMPLETED 0 2022-04-08 17:10:07.336 1.5s 110ms 11.3% 0 0 323.4 KB 23 KB
49 0e/277efb 1387 base_freq (7) COMPLETED 0 2022-04-08 17:10:07.431 1.4s 117ms 11.4% 0 0 325.8 KB 25.5 KB
48 d7/6b0278 1357 base_freq (6) COMPLETED 0 2022-04-08 17:10:07.412 1.5s 108ms 11.0% 0 0 323.6 KB 23.3 KB
46 ec/0a40f8 1325 goalign (1) COMPLETED 0 2022-04-08 17:10:07.393 2s 850ms 15.7% 3 MB 14 MB 622.1 KB 796.1 KB
50 6c/a97f2f 1898 base_freq (8) COMPLETED 0 2022-04-08 17:10:08.797 1.1s 109ms 12.5% 0 0 324 KB 23.7 KB
51 24/50dcea 2231 report2 COMPLETED 0 2022-04-08 17:10:10.954 942ms 34ms 12.8% 0 0 131.8 KB 2 KB
42 11/eec7a7 1234 logo (1) COMPLETED 0 2022-04-08 17:10:07.315 7s 6s 45.7% 171.9 MB 309.9 MB 13.8 MB 1002.7 KB
43 dd/4c93e5 2536 logo (2) COMPLETED 0 2022-04-08 17:10:14.327 6.1s 5.4s 50.4% 168.4 MB 306.8 MB 13.8 MB 853.1 KB
45 9f/711bb8 2970 logo (4) COMPLETED 0 2022-04-08 17:10:20.444 6.1s 5.4s 50.6% 169 MB 307.3 MB 13.8 MB 873.9 KB
44 cf/a776a3 3401 logo (3) COMPLETED 0 2022-04-08 17:10:26.591 6.1s 5.4s 50.4% 169.4 MB 307.6 MB 13.8 MB 883.3 KB
52 1f/a2f030 3833 global_logo (1) COMPLETED 0 2022-04-08 17:10:32.704 6.5s 5.8s 53.8% 169.9 MB 307.2 MB 13.8 MB 846.9 KB
53 1c/011595 4270 global_logo (2) COMPLETED 0 2022-04-08 17:10:39.184 6.6s 5.8s 53.3% 171.2 MB 308.4 MB 13.8 MB 922.1 KB
54 7f/cf75ca 4714 print_report (1) COMPLETED 0 2022-04-08 17:10:46.299 10.6s 9.8s 43.1% 302.4 MB 1 TB 51 MB 25.6 MB
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