Reconstruct bed file out of columns

Question

[dzisis1986]

Hello i have a bed file like this

1   3004104 3004110
1   3005819 3005825
1   3008315 3008321 
1   3008893 3008899  
1   3009812 3009818 
1   3012422 3012428  
1   3015794 3015800  
1   3016183 3016189 
1   3024019 3024025 
1   3025279 3025285

and i would like to create another one out of this to in this format :

1   1   3004110
1   3004104 3005825
1   3005819 3008321
1   3008315 3008899
1   3008893 3009818
1   3009812 3012428
1   3012422 3015800
1   3015794 3016189
1   3016183 3024025
1   3024019 3025285

Do you know an easy way to do it in R or in Python ?

Thank you in advance

[Pierre Lindenbaum]

what have you tried ?

[dzisis1986]

I tried R i can read each column but i can't create a for loop as i want in order to select each time the 2nd column as start and the next row 3rd column as end position

[zx8754]

Is bed file per chromosome?

[dzisis1986]

Yes it is a bed file with chr-start-end

[zx8754]

What happened to the last row? 1 3025279 3025285

[dzisis1986]

i was thinking about the same but the last row stays like that .. 1 3024019 3025285 The 3025279 postion is into the rage above so no more line needed

Answer 1

[zx8754]

Using R, lag function from dplyr package:

# example data
mybed <- read.table(text = "
                    1   3004104 3004110
                    1   3005819 3005825
                    1   3008315 3008321 
                    1   3008893 3008899  
                    1   3009812 3009818 
                    1   3012422 3012428  
                    1   3015794 3015800  
                    1   3016183 3016189 
                    1   3024019 3024025 
                    1   3025279 3025285")


library(dplyr)

mybed %>% 
  transmute(
    chr = V1,
    start = lag(V2, default = 1),
    end = V3)

Answer 2

[Bastien Hervé]

In python :

new_bed = open("new_bed_file.bed", 'a')

new_chrom=""
with open("bed_file.bed", 'r') as bed_f:
    for line in bed_f:
        if new_chrom != line.split("\t")[0]:
            first_line=True
            if first_line:
                new_bed.write('\t'.join([line.split("\t")[0],"1",line.split("\t")[2]]))
                first_line=False
            else:
                new_bed.write('\t'.join([line.split("\t")[0],new_position,line.split("\t")[2]]))
            new_chrom = line.split("\t")[0]
            new_position=line.split("\t")[1]

As said in comment you will lose the last row !