2_cleanFilenames.Rmd

---
title: "separteFileNames"
author: "Gaurav"
date: "12/15/2019"
output: html_document
---

```{r setup, include=FALSE}
files <- read.table('SCTCfiles.txt',stringsAsFactors = F)
```
Split files in groups
```{r}
colnames(files)[1] <- 'fileName' 
group <- sapply(1:nrow(files),function(i) paste0(strsplit(files[i,1],'_')[[1]][2:3],collapse = '_'))
files$group <- group
spltFiles <- split(files,files$group)
```
Sort names with group for downstream kb analysis
```{r}
for(i in 1:length(spltFiles)){
      if (nrow(spltFiles[[i]]) > 3){
            fnames <- spltFiles[[i]]$fileName
            fodrStr <- sapply(fnames,function(fn) paste0(strsplit(fn,'_')[[1]][c(5,4)],collapse = ''))
            spltFiles[[i]] <- spltFiles[[i]][order(fodrStr),]
      }
}
```
Save group files
```{r}
for(i in 1:length(spltFiles)){
      write.table(spltFiles[[i]][,1],file=paste0('files/',spltFiles[[i]][1,2],'.txt'),quote = F,row.names = F,col.names = F)
}
```