Reconstruct bed file out of columns
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
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zx8754
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dzisis1986 •
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written
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dzisis1986 •
2 answers
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)
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 !
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Bastien Hervé
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Reconstruct bed file from tab
written by dzisis1986 •
what have you tried ?
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
Is bed file per chromosome?
Yes it is a bed file with chr-start-end
What happened to the last row?
1 3025279 3025285i 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