R sort list of files numerically

Question

I have a list of files that I need to sort numerically, such that I can import them in order

my code is:

bed = '/files/coverage_v2'

beds=list.files(path=bed, pattern='ctcf.motif.minus[0-9]+.bed.IGTB950.bed')
for(b in beds){
`for(b in beds){`print(b)

  read.table(b)

}

> [1] "ctcf.motif.minus1.bed.IGTB950.bed"   "ctcf.motif.minus10.bed.IGTB950.bed" 
 [3] "ctcf.motif.minus100.bed.IGTB950.bed" "ctcf.motif.minus101.bed.IGTB950.bed"
 [5] "ctcf.motif.minus102.bed.IGTB950.bed" "ctcf.motif.minus103.bed.IGTB950.bed"
 [7] "ctcf.motif.minus104.bed.IGTB950.bed" "ctcf.motif.minus105.bed.IGTB950.bed"
 [9] "ctcf.motif.minus106.bed.IGTB950.bed" "ctcf.motif.minus107.bed.IGTB950.bed"
[11] "ctcf.motif.minus108.bed.IGTB950.bed" "ctcf.motif.minus109.bed.IGTB950.bed"
[13] "ctcf.motif.minus11.bed.IGTB950.bed"  "ctcf.motif.minus110.bed.IGTB950.bed"
[15] "ctcf.motif.minus111.bed.IGTB950.bed" "ctcf.motif.minus112.bed.IGTB950.bed"
[17] "ctcf.motif.minus113.bed.IGTB950.bed" "ctcf.motif.minus114.bed.IGTB950.bed"
[19] "ctcf.motif.minus115.bed.IGTB950.bed" "ctcf.motif.minus116.bed.IGTB950.bed"
[21] "ctcf.motif.minus117.bed.IGTB950.bed" "ctcf.motif.minus118.bed.IGTB950.bed"
[23] "ctcf.motif.minus119.bed.IGTB950.bed" "ctcf.motif.minus12.bed.IGTB950.bed" 
[25] "ctcf.motif.minus120.bed.IGTB950.bed" "ctcf.motif.minus121.bed.IGTB950.bed"
[27] "ctcf.motif.minus122.bed.IGTB950.bed" "ctcf.motif.minus123.bed.IGTB950.bed"
[29] "ctcf.motif.minus124.bed.IGTB950.bed" "ctcf.motif.minus125.bed.IGTB950.bed"
[31] "ctcf.motif.minus126.bed.IGTB950.bed" "ctcf.motif.minus127.bed.IGTB950.bed"
[33] "ctcf.motif.minus128.bed.IGTB950.bed" "ctcf.motif.minus129.bed.IGTB950.bed"
[35] "ctcf.motif.minus13.bed.IGTB950.bed"  "ctcf.motif.minus130.bed.IGTB950.bed"
[37] "ctcf.motif.minus131.bed.IGTB950.bed" "ctcf.motif.minus132.bed.IGTB950.bed"
[39] "ctcf.motif.minus133.bed.IGTB950.bed" "ctcf.motif.minus134.bed.IGTB950.bed"

But what I really want is for it to be sorted numerically:

> "ctcf.motif.minus1.bed.IGTB950.bed" 
"ctcf.motif.minus10.bed.IGTB950.bed" 
"ctcf.motif.minus11.bed.IGTB950.bed"
"ctcf.motif.minus12.bed.IGTB950.bed" 
"ctcf.motif.minus13.bed.IGTB950.bed"
"ctcf.motif.minus100.bed.IGTB950.bed"
"ctcf.motif.minus101.bed.IGTB950.bed"

etc, so that it will be imported numerically.

Thanks in advance!!

akrun · Accepted Answer · 2015-04-19T17:28:34.913

You could try mixedsort from gtools

library(gtools)
beds1 <- mixedsort(beds)
head(beds1)
#[1]"ctcf.motif.minus1.bed.IGTB950.bed"   "ctcf.motif.minus10.bed.IGTB950.bed" 
#[3]"ctcf.motif.minus11.bed.IGTB950.bed"  "ctcf.motif.minus12.bed.IGTB950.bed" 
#[5]"ctcf.motif.minus13.bed.IGTB950.bed"  "ctcf.motif.minus100.bed.IGTB950.bed"

Or using regex (assuming that the order depends on the numbers after 'minus' and before 'bed'.

beds[order(as.numeric(gsub('\\D+|\\.bed.*', '', beds)))]

R sort list of files numerically

1 Answers1