Matching position and output neighbors within 500 distant Post: 302884169

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Top Forums UNIX for Dummies Questions & Answers Matching position and output neighbors within 500 distant Post 302884169 by fat on Saturday 18th of January 2014 03:12:38 AM

01-18-2014

Registered User

Quote:

Originally Posted by migurus

awk based solution

Code:

 
 $ cat test.sh
 awk '
{
        if (NR == FNR)  ### reading 1st file
                        ### accumulate 2nd column values in array of key values
        {
                arr[NR] = $2;
        }
        else            ### reading 2nd file and check for value of 2nd column
                        ### to be within +/- 500 of any accumulated key values
        {
                maxval = $2 + 500;
                minval = $2 - 500;
                for ( x in arr )
                {
                        if(minval <= arr[x] && arr[x] <= maxval)
                                print $0;
                }
         }
}
' $1 $2

Here is how I ran it

Code:

 
 $ cat a
1       11567687        snpid20
1       153881  snpid1
2       56768799        snpid7
3       3156760 snpid4
3       1567687 snpid7
$ cat b
1       11567600        snpid20
3       1000000 snpid7
 $ test.sh b a
 1       11567687        snpid20

hope this is what you were looking for

Thanks
This almost works except that it outputs all +/- 500 range of the keys. for example when searching for +/- 500 of the key 11567687 in "1 11567687 snpid20" it should output all values +/- 500 from second file that have their column 1 as 1, when searching for +/- 500 of key 3156760 "3 3156760 snpid4" it should output all values +/- 500 from second file that have their column 1 as 3.

fat

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LEARN ABOUT DEBIAN

vcf-isec

VCF-ISEC(1)							   User Commands						       VCF-ISEC(1)

NAME

       vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

SYNOPSIS

       vcf-isec [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.

	      Note that lines from all files can be intermixed together on the output, which can yield unexpected results.

OPTIONS

       -C, --chromosomes <list|file>
	      Process the given chromosomes (comma-separated list or one chromosome per line in a file).

       -c, --complement
	      Output positions present in the first file but missing from the other files.

       -d, --debug
	      Debugging information

       -f, --force
	      Continue even if the script complains about differing columns.

       -o, --one-file-only
	      Print only entries from the left-most file. Without -o, all unique positions will be printed.

       -n, --nfiles [+-=]<int>
	      Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.

       -p, --prefix <path>
	      If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)

       -t, --tab <chr:pos:file>
	      Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)

       -w, --win <int>
	      In  repetitive  sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

EXAMPLES

	      bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz

vcf-isec 0.1.5							     July 2011							       VCF-ISEC(1)

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