Commit cd77d3af authored by Raphael Müller's avatar Raphael Müller
Browse files

removed unnecessary scripts

parent 02c7302f
#!/usr/bin/env python3
import sys
# Reading file
assembFile = sys.argv[1]
# Variable for assembly length
assembLen = 0
# Opening file
with open (assembFile, 'r') as aF:
# Reading each line
for line in aF:
# Each line that does not start with ">"
if not line.startswith(">"):
assembLen = assembLen + len(line.strip())
print(assembLen)
#!/usr/bin/env python3
import sys
# Reading files
#!/usr/bin/env Rscript
library(ggplot2)
options(scipen=999)
# Set up variable to control command line arguments
args <- commandArgs(TRUE)
files <- c(args)
techs <- list()
for(i in 1:length(files)){
if (grepl("pb_sort_cov_hist", files[i], fixed = TRUE)){
techs.current <- "PacBio"
} else if (grepl("ont_sort_cov_hist", files[i], fixed = TRUE)){
techs.current <- "Nanopore"
} else {
techs.current <- "Illumina"
}
techs[i] <- techs.current
}
df <- data.frame()
for(i in 1:length(files)){
df.current <- read.table(files[i])
df.current$tech <- techs[i]
df <- rbind(df,df.current)
}
df$tech <- factor(unlist(df$tech, use.names = TRUE))
colnames(df) <- c("Coverage","Count","tech")
p <- ggplot(data = df, mapping = aes(x = Coverage, y = Count, group = tech, color = tech)) +
geom_line() +
annotation_logticks() +
scale_x_log10() +
expand_limits(x = 0, y = 0)
ggsave("Rall.jpeg", plot = p, device = "jpeg")
# scale_y_log10() +
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