how to convert a txt file to bed file

Question

[evafinegan]

Hello,

I have a text file and I want to convert it to a bed file. My text file looks like:

S_12g0010.2.1:0-170
S_12g0030.2.1:0-476
S_12g0040.2.1:0-94
S_12g0080.2.1:0-259
S_12g0020.2.1:0-382

Can anyone suggest a way for this conversion. Thank you!

[Pierre Lindenbaum]

Can anyone suggest a way for this conversion.

tr

Answer 1

[JC]

First, check the format definition

Second, use [tr, sed, perl] to convert this, like:

perl -pe 's/:/\t/; s/-(\d+)$/\t$1/' < in.txt < in.txt > out.bed

Edit: updated to support "-" in sequence name

[evafinegan]

Thank you, I have used your suggestion. It made a bed file but I see some strange things in some of the lines:

S_12g00500.1.1  0   273
S_12g0000.1 c2.1    0-210

I think the second line should look like this:

  S_12g0000.1c2.1   0 210

The original line in txt file looks like this:

S_12g0000.1-c2.1:0-210

[JC]

are you sure you use the same input/command?

$ cat > in.txt
S_12g0010.2.1:0-170
S_12g0030.2.1:0-476
S_12g0040.2.1:0-94
S_12g0080.2.1:0-259
S_12g0020.2.1:0-382

$ perl -pe "s/:/\t/; s/-/\t/" < in.txt
S_12g0010.2.1   0       170
S_12g0030.2.1   0       476
S_12g0040.2.1   0       94
S_12g0080.2.1   0       259
S_12g0020.2.1   0       382

[JC]

I see you have a "-" in the sequence id, to avoid that you can use:

perl -pe "s/:/\t/; s/-(\d+)$/\t$1/"

[evafinegan]

Using this the output is:

S_12g0010.2.1   0       
S_12g0030.2.1   0      
S_12g0040.2.1   0       
S_12g0080.2.1   0       
S_12g0020.2.1   0       
S_12g0000.1-c2.1    0

Now there is no third column,

[evafinegan]

This works: perl -pe "s/:/\t/; s/-(\d+)$/\t\1/" Thank you!

[evafinegan]

Yes, I have used the same command that you suggested. So my input text file has some of the lines like this:

S_12g0010.2.1:0-170
S_12g0030.2.1:0-476
S_12g0040.2.1:0-94
S_12g0080.2.1:0-259
S_12g0020.2.1:0-382    
S_12g0000.1-c2.1:0-210

Your suggestion works well for rest of the lines except the last line where I get output like:

S_12g0010.2.1   0       170
S_12g0030.2.1   0       476
S_12g0040.2.1   0       94
S_12g0080.2.1   0       259
S_12g0020.2.1   0       382
S_12g0000.1 c2.1    0-210

[JC]

$ cat > in.txt
S_12g0010.2.1:0-170
S_12g0030.2.1:0-476
S_12g0040.2.1:0-94
S_12g0080.2.1:0-259
S_12g0020.2.1:0-382
S_12g0000.1-c2.1:0-210
$ perl -pe 's/:/\t/; s/-(\d+)$/\t$1/' < in.txt
S_12g0010.2.1   0       170
S_12g0030.2.1   0       476
S_12g0040.2.1   0       94
S_12g0080.2.1   0       259
S_12g0020.2.1   0       382
S_12g0000.1-c2.1        0       210

[Ram]

@JC: Please update your answer with the one that accounts for -s in seq IDs

@evafinegan: Once JC updates it, please accept the answer using the green check mark below the upvote button: