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