Hi, now I have two bed files. Each have four columuns, and the fourth column has the uniq ID for each row, each file has thousands of rows. Now I want to combine row of the two files if the rows have the same ID, the final output should like this:
chr1 10028 10029 chr14 68314662 68314663 J00118:253:HJ2FTBBXX:3:2213:8491:13394
bed 1:
chr1 10028 10029 J00118:253:HJ2FTBBXX:3:2213:8491:13394
...
bed 2:
chr14 68314662 68314663 J00118:253:HJ2FTBBXX:3:2213:8491:13394
...
•
written
by
szp770 •
4 answers
save below text to combine_bed_by_id.pl, then perl combine_bed_by_id.pl bed1.txt bed2.txt
use strict;
use warnings;
my ($bed1, $bed2) = @ARGV;
my %bed1 = read_bed($bed1);
my %bed2 = read_bed($bed2);
for my $id (sort keys %bed1){
print "$bed1{$id}\t$bed2{$id}\t$id\n" if $bed2{$id};
}
sub read_bed{
my $bed=shift;
open IN,"$bed";
my %f;
while(<IN>){
chomp;
my @temp = split;
my $id = pop @temp;
my $info = join "\t", @temp;
$f{$id} = $info;
}
return %f;
close IN;
}
•
written
by
wangmingcheng1992 •
join -t $'\t' -1 4 -2 4 <(sort -t $'\t' -k4,4 file1.bed) <(sort -t $'\t' -k4,4 file2.bed)
... and the simplest I would go for. Considering that join output provides the ID in the first column, here's a minimum modification to exactly match the desired output:
join -t $'\t' -1 4 -2 4 <(sort -k4,4 file1.bed) <(sort -k4,4 file2.bed) | perl -pe 's/(\S+)\t(.+)/$2\t$1/'
here's a minimum modification to exactly match the desired output:
you can use the formatting option of join -o FORMAT to achieve the same result ;-)
Good to know. Thank you Pierre.
Pierre's answer would still work. It'll output columns 4, 1-3 and 5 of the first file, plus 1-3 and 5 of the second file. As Pierre mentioned, you may modify the column layout using the -o option. Here's an example that may help you understand hoy join output format works.
perl -lane '$d{$F[3]} .= "@F[0..2] "; END {
foreach $i (keys %d) { print $d{$i}.$i }
}' file1.bed file2.bed | awk '$5~/./'
Here's one that might be a little simpler to follow:
$ sort -k4,4 A.bed B.bed | paste -d "\t" - - | cut -f1-3,5-8 | sort-bed - > answer.bed
Here's how it works:
sort -k4,4 A.bed B.bed - sort the concatenation of A and B by the fourth column
paste -d "\t" - - - take every two lines from the output of sort and join them by a tab character
cut -f1-3,5-8 - take columns 1 through 3 and 5 through 8 of the output from paste
sort-bed - - sort the output lexicographically for downstream set operations
Any pure sorting solution will only work if both files contain the same IDs and nothing else, as it will pair every 2 lines independently on their ID. A previous selection of IDs present in both files should be performed before using this code. Here's an example nesting 2 cut | grep, one to detect shared IDs and the other to print only lines containing those IDs:
cut -f4 A.bed | grep -F -f - B.bed | cut -f4 | grep -h -F -f - A.bed B.bed \
| sort -k4,4 | paste -d "\t" - - | cut -f1-3,5-8 | sort-bed - > answer.bed
... although this is basically what the join solution does.
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