Merging two files with condition on two columns - perl

Question

I have two files of the type:
File1.txt
1 117458 rs184574713 rs184574713
1 119773 rs224578963 rs224500000
1 120000 rs224578874 rs224500045
1 120056 rs60094200 rs60094200
2 120056 rs60094536 rs60094536
File2.txt
10 120200 120400 A 0 189,183,107
1 0 119600 C 0 233,150,122
1 119600 119800 D 0 205,92,92
1 119800 120400 F 0 192,192,192
2 120400 122000 B 0 128,128,128
2 126800 133200 A 0 192,192,192
I want to add the information contained in the second file to the first file. The first column in both files needs to match, while the second column in File1.txt should fall in the interval that is indicated by columns 2 and 3 in File2.txt. So that the output should look like this:
1 117458 rs184574713 rs184574713 C 0 233,150,122
1 119773 rs224578963 rs224500000 D 0 205,92,92
1 120000 rs224578874 rs224500045 F 0 192,192,192
1 120056 rs60094200 rs60094200 F 0 192,192,192
2 120440 rs60094536 rs60094536 B 0 128,128,128
Please help me with awk/perl.. or any other script.

Answer 1

This is how you would do it in bash (with a little help from awk):
join -1 1 -2 1 \
<(sort -n -k1,1 test1) <(sort -n -k1,1 test2) | \
awk '$2 >= $5 && $2 <= $6 {print $1, $2, $3, $4, $7, $8, $9}'
Here is a brief explanation.
First, we use join to join lines based on the common key (the
first field).
But join expects both input files to be already sort (hence
sort).
At least, we employ awk to apply the required condition, and to
project the fields we want.

Answer 2

Try this: (Considering the fact that there is a typo in your output for last entry. 120056 is not between 120400 122000.
$ awk '
NR==FNR {
a[$1,$2,$3]=$4 FS $5 FS $6;
next
}
{
for(x in a) {
split(x,tmp,SUBSEP);
if($1==tmp[1] && $2>=tmp[2] && $2<=tmp[3])
print $0 FS a[x]
}
}' file2 file1
1 117458 rs184574713 rs184574713 C 0 233,150,122
1 119773 rs224578963 rs224500000 D 0 205,92,92
1 120000 rs224578874 rs224500045 F 0 192,192,192
1 120056 rs60094200 rs60094200 F 0 192,192,192
You read through the first file creating an array indexed at column 1,2 and 3 having values of column 4,5 and 6.
For the second file, you look up in your array. For every key, you split the key and check for your condition of first column matching and second column to be in range.
If the condition is true you print the entire line from file 1 followed by the value of array.