In [1]:

    

%load_ext rpy2.ipython
%Rdevice svg


    

In [2]:

    

%%R
library(ape)
library(magrittr)
library(phangorn)
library(adephylo)


    

    






Loading required package: ade4

Attaching package: ‘adephylo’

The following object is masked from ‘package:ade4’:

    orthogram

In [10]:

    

%%R
regionaldirstub <- "../rawdata/november2014/HPTN071/replicates"
regionaldirs <- list.dirs(regionaldirstub)
regionaldirs <- regionaldirs[2:length(regionaldirs)]
stubs <- strsplit(regionaldirs,"/") %>% lapply(.,tail,1) %>% unlist
numsc <- length(stubs)


    

    






 [1] "281014_HPTN071_scA_rep10_SIMULATED" "281014_HPTN071_scA_rep11_SIMULATED"
 [3] "281014_HPTN071_scA_rep12_SIMULATED" "281014_HPTN071_scA_rep13_SIMULATED"
 [5] "281014_HPTN071_scA_rep14_SIMULATED" "281014_HPTN071_scA_rep15_SIMULATED"
 [7] "281014_HPTN071_scA_rep16_SIMULATED" "281014_HPTN071_scA_rep17_SIMULATED"
 [9] "281014_HPTN071_scA_rep18_SIMULATED" "281014_HPTN071_scA_rep19_SIMULATED"
[11] "281014_HPTN071_scA_rep20_SIMULATED" "281014_HPTN071_scA_rep2_SIMULATED" 
[13] "281014_HPTN071_scA_rep3_SIMULATED"  "281014_HPTN071_scA_rep4_SIMULATED" 
[15] "281014_HPTN071_scA_rep5_SIMULATED"  "281014_HPTN071_scA_rep6_SIMULATED" 
[17] "281014_HPTN071_scA_rep7_SIMULATED"  "281014_HPTN071_scA_rep8_SIMULATED" 
[19] "281014_HPTN071_scA_rep9_SIMULATED"  "281014_HPTN071_scB_rep10_SIMULATED"
[21] "281014_HPTN071_scB_rep11_SIMULATED" "281014_HPTN071_scB_rep12_SIMULATED"
[23] "281014_HPTN071_scB_rep13_SIMULATED" "281014_HPTN071_scB_rep14_SIMULATED"
[25] "281014_HPTN071_scB_rep15_SIMULATED" "281014_HPTN071_scB_rep16_SIMULATED"
[27] "281014_HPTN071_scB_rep17_SIMULATED" "281014_HPTN071_scB_rep18_SIMULATED"
[29] "281014_HPTN071_scB_rep19_SIMULATED" "281014_HPTN071_scB_rep20_SIMULATED"
[31] "281014_HPTN071_scB_rep2_SIMULATED"  "281014_HPTN071_scB_rep3_SIMULATED" 
[33] "281014_HPTN071_scB_rep4_SIMULATED"  "281014_HPTN071_scB_rep5_SIMULATED" 
[35] "281014_HPTN071_scB_rep6_SIMULATED"  "281014_HPTN071_scB_rep7_SIMULATED" 
[37] "281014_HPTN071_scB_rep8_SIMULATED"  "281014_HPTN071_scB_rep9_SIMULATED" 
[39] "281014_HPTN071_scC_rep10_SIMULATED" "281014_HPTN071_scC_rep11_SIMULATED"
[41] "281014_HPTN071_scC_rep12_SIMULATED" "281014_HPTN071_scC_rep13_SIMULATED"
[43] "281014_HPTN071_scC_rep14_SIMULATED" "281014_HPTN071_scC_rep15_SIMULATED"
[45] "281014_HPTN071_scC_rep16_SIMULATED" "281014_HPTN071_scC_rep17_SIMULATED"
[47] "281014_HPTN071_scC_rep18_SIMULATED" "281014_HPTN071_scC_rep19_SIMULATED"
[49] "281014_HPTN071_scC_rep20_SIMULATED" "281014_HPTN071_scC_rep2_SIMULATED" 
[51] "281014_HPTN071_scC_rep3_SIMULATED"  "281014_HPTN071_scC_rep4_SIMULATED" 
[53] "281014_HPTN071_scC_rep5_SIMULATED"  "281014_HPTN071_scC_rep6_SIMULATED" 
[55] "281014_HPTN071_scC_rep7_SIMULATED"  "281014_HPTN071_scC_rep8_SIMULATED" 
[57] "281014_HPTN071_scC_rep9_SIMULATED" 

In [13]:

    

%%R
genes <- c("gag","pol","env")
seqdata <- list()
for(i in 1:numsc){
    for(j in 1:length(genes)){
        if(j==1){
            s <- read.dna(paste(regionaldirs[i],"/",stubs[i],"_",genes[j],".fa",sep=""),format="fasta",as.matrix=TRUE)
            snames <- row.names(s)
            o <- order(snames)
            snames <- snames[o]
            s <- s[o,]
        }else{
            s2 <- read.dna(paste(regionaldirs[i],"/",stubs[i],"_",genes[j],".fa",sep=""),format="fasta",as.matrix=TRUE)
            s2names <- row.names(s2)
            o <- order(s2names)
            s2names <- s2names[o]
            s <- cbind(s,s2[o,])
        }
    }
    seqdata[[i]] <- s
}


    

In [14]:

    

%%R
seqnames.fn <- paste(stubs,".fas",sep="")
for(i in 1:numsc){
    write.dna(seqdata[[i]],seqnames.fn[i],format="fasta",nbcol=-1,colsep="")
}