overlapped genomic coordinates


 
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# 1  
overlapped genomic coordinates

Hi,

I would like to know how can I get the ID of a feature if its genomic coordinates overlap the coordinates of another file. Example:

Get the 4th column (ID) of this file1:
Code:
chr1	10	100	gene1
chr2	3000	5000	gene2
chr3	200	1500	gene3

if it overlaps with a feature in this file2:
Code:
chr2 3001 3330
chr4 10 100

Desired output file:
Code:
chr2 3001 3330 gene2


Thanks in advance
# 2  
So, we have a = key, a min key, a max key and a payload field. Sorting helps. Unix tools are not so good at merging not=equal. Shell solution tend toward putting one file into an array and then using it to filter the other, which does not scale well. If the first field is reasonably selective, an 'join' of two sorted files gives you the cartesian product lines, which you can read in shell from a pipe and decide if they are a hit. Man Page for join (linux Section 1) - The UNIX and Linux Forums
Code:
sort -o file1 file1
sort -o file2 fiel2
join file1 file2 | whille read f1 f1a f1b f1c f2b f3b f4b
do
 if (( ( $f2a <= $f2b
     && $f3a >= $f2b )
    || ( $f2a <= $f3b
     && $f3a >= $f3b ) ))
 then
  echo $f1 $f2b $f3b $f4b
 fi
done

 

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