From 098c0efe8e5870bed6417c34b7b71db8f4fd87b1 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Mon, 17 Jun 2024 16:15:27 +0200
Subject: [PATCH] read all trace files and plot benchmark (to clean)
---
benchmark/open_traces.py | 6 ++++
benchmark/plots.r | 68 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 74 insertions(+)
create mode 100755 benchmark/open_traces.py
create mode 100644 benchmark/plots.r
diff --git a/benchmark/open_traces.py b/benchmark/open_traces.py
new file mode 100755
index 0000000..e264b29
--- /dev/null
+++ b/benchmark/open_traces.py
@@ -0,0 +1,6 @@
+import polars as pl
+from pathlib import Path
+files = list(Path("./wt_AD281").glob("*/pipeline_info/*.txt"))
+list_df = [pl.read_csv(file, separator="\t").with_columns(file=pl.lit(str(file))).select(pl.all().cast(pl.Utf8)) for file in files]
+df = pl.concat(list_df)
+df.write_csv("recap.txt", separator="\t")
diff --git a/benchmark/plots.r b/benchmark/plots.r
new file mode 100644
index 0000000..13dd0f2
--- /dev/null
+++ b/benchmark/plots.r
@@ -0,0 +1,68 @@
+install.packages("tidyverse")
+install.packages("ggplot2")
+library(tidyverse)
+library(ggplot2)
+library(dplyr)
+
+df <- read.csv("/home/mcroiset/HiC/benchmark/recap.txt", sep = "\t", header = TRUE)
+
+convert_time <- function(x){
+ parts <- strsplit(x, " ")
+ list_durations <- character(0)
+ for( part in parts ) {
+ sec <- 0
+ minute <- 0
+ hours <- 0
+ for ( single in part ) {
+ if (grepl('s', single, fixed = TRUE)) {
+ sec <- as.numeric(substr(single,1,nchar(single)-1))
+ sec <- sec/60
+ sec <- as.numeric(format(round(sec, 3), nsmall = 3))
+ #print(sec)
+ }
+ if (grepl('m', single, fixed = TRUE)) {
+ minute <- as.numeric(substr(single,1,nchar(single)-1))
+ minute <- as.numeric(format(round(minute, 2), nsmall = 2))
+ #print(minute)
+ }
+ if (grepl('h', single, fixed = TRUE)) {
+ hours <- as.numeric(substr(single,1,nchar(single)-1))
+ hours <- hours*60
+ hours <- as.numeric(format(round(hours, 2), nsmall = 2))
+ #print(hours)
+ #print(single)
+ }
+ #print(sec)
+ #print(minute)
+ #print(hours)
+ }
+ new_duration <- (hours+minute+sec)
+ list_durations <- append(list_durations,new_duration)
+ #print(new_duration)
+ #print(df$duration[i])
+ #df$duration[i] <- new_duration
+ }
+ #print(list_durations)
+ return(list_durations)
+}
+
+list_dur <- convert_time(df$duration)
+df$duration
+
+df$duration_minutes <- list_dur
+df$duration_minutes <- as.numeric(df$duration_minutes)
+
+val <- df %>% group_by(name) %>% summarise(moy = mean(duration_minutes), ect = sd(duration_minutes))
+
+ggplot(df, aes(x=name, y=duration_minutes))+
+ geom_violin()+
+ ylim(0,500)+
+ facet_wrap(~ name, ncol = 8)
+
+
+# for (x in df$duration_minutes) {
+# print(class(x))
+# }
+
+# mean(df$duration_minutes)
+# sd(df$duration_minutes)
--
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