Regular Expression To Match Bed Format

Question

[Boboppie]

I see a TAB delimited parser, but I have to be restrict on the first three columns (chr, start, end), and since the rest of the columns are optional, they might not be available in the data at all.

I came up with: [^\t]+\t\d+\t\d+\t?.|[^\t]+\t\d+\t\d+$

However I'm not really convinced by myself.

Any better suggestions?

[Pierre Lindenbaum]

I think your regex is OK. You could insert a '^' as the first character to match the beginning of the line.

[Pablo]

If it's perl you might just use something like ($chr, $start, $end) = split /t/;

[Boboppie]

@Pierre, good point, cheers.