Module: ViralSeq

Defined in:

lib/viral_seq.rb,
lib/viral_seq/pid.rb,
lib/viral_seq/math.rb,
lib/viral_seq/sdrm.rb,
lib/viral_seq/hivdr.rb,
lib/viral_seq/muscle.rb,
lib/viral_seq/tcs_dr.rb,
lib/viral_seq/recency.rb,
lib/viral_seq/ref_seq.rb,
lib/viral_seq/version.rb,
lib/viral_seq/constant.rb,
lib/viral_seq/seq_hash.rb,
lib/viral_seq/sequence.rb,
lib/viral_seq/tcs_core.rb,
lib/viral_seq/tcs_json.rb,
lib/viral_seq/rubystats.rb,
lib/viral_seq/seq_hash_pair.rb

Overview

lib/version.rb version info and histroy

Defined Under Namespace

Modules: Math, Muscle, PID, Recency, RefSeq, Rubystats Classes: DRMs, SeqHash, SeqHashPair, Sequence, TcsCore, TcsDr, TcsJson

Constant Summary

VERSION =

"1.3.0"

TCS_VERSION =

"2.3.8"

AMINO_ACID_LIST =

array for all amino acid one letter abbreviations

["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y", "*"]

R_SCRIPT_CHECK_PACKAGES =

R script to check if the required libraries are installed, if not, install the missing libraries

'dir.create(path = Sys.getenv("R_LIBS_USER"), showWarnings = FALSE, recursive = TRUE);' +
'packages <- c("ggplot2", "phangorn", "ape", "scales", "ggforce", "cowplot", "magrittr", "gridExtra");' +
'install.packages(setdiff(packages, rownames(installed.packages())), lib = Sys.getenv("R_LIBS_USER"), repos = "https://cran.rstudio.com/")'

R_SCRIPT =

R script for tcs_sdrm script

'setwd("PATH_TO_FASTA")
library(phangorn)
library(ape)
library(ggplot2)
library(scales)
library(ggforce)
library(cowplot)
library(magrittr)
library(gridExtra)
pdf("OUTPUT_PDF", onefile=T, width=11, height=8.5)
fileNames <- list.files()
for (fileName in fileNames) {
dna <- read.dna(fileName, format="fasta")
class(dna)
D<- dist.dna(dna, model="raw")
pi <- mean(D)
dist20 <- quantile(D, prob=c(0.20))
alldist <- data.frame(File=fileName, pi, dist20)
write.table(alldist,"OUTPUT_CSV",append=TRUE, sep = ",", row.names = FALSE, col.names=FALSE)
D2 <- dist.dna(dna, model="TN93")*100
def.par <- par(no.readonly = TRUE)
par(mfrow=c(1,2))
hist<-hist(D, main=fileName, xlab="% Pairwise Distance", ylab="Frequency", col="gray")
abline(v=dist20, col="royalblue",lwd=2)
abline(v=pi, col="red", lwd=2)
legend(x="topright", c("dist20", "pi"), col = c("royalblue", "red"), lwd = c(2,2), cex=0.5)
njtree<-NJ(D2)
njtreeplot <- plot(njtree, show.tip.label=F, "unrooted", main=fileName)
add.scale.bar(cex=0.7, font=2, col="red")
}
dev.off()'