Question: Extracting similar ssrs from two different misa files
0
gravatar for kartikayprasad
4 months ago by
kartikayprasad10 wrote:

Hello friends, I have two misa file, i want to extract those lines which are showing similar ssrs from both the files. for example: File1:

ID  SSR nr. SSR type    SSR size    start   end
P_S1_L001_R1_001_(paired)_150721_contig_1   1   p1  (T)11   11  905 915
P_S1_L001_R1_001_(paired)_150721_contig_1   2   p1  (A)11   11  2102    2112
P_S1_L001_R1_001_(paired)_150721_contig_1   3   p1  (A)11   11  3020    3030
P_S1_L001_R1_001_(paired)_150721_contig_1   4   p1  (T)12   12  3361    3372
P_S1_L001_R1_001_(paired)_150721_contig_1   5   p2  (CT)6   12  3944    3955

File2:

ID  SSR nr. SSR type    SSR size    start   end
P_S1_L001_R1_001_1_(paired)_150727_contig_10    1   p1  (A)10   10  5047    5056
P_S1_L001_R1_001_1_(paired)_150727_contig_10    2   p1  (T)10   10  9828    9837
P_S1_L001_R1_001_1_(paired)_150727_contig_10    3   p1  (A)10   10  11634   11643
P_S1_L001_R1_001_1_(paired)_150727_contig_10    4   p2  (TC)7   14  17272   17285

i want to extract those lines which are common in both the files on the basis of ssrs and print both the files with tab separated format in new file

output:

 P_S1_L001_R1_001_(paired)_150721_contig_1  1   p1  (T)11   11  905 915 P_S1_L001_R1_001_1_(paired)_150727_contig_10    2   p1  (T)10   10  9828    9837

P_S1_L001_R1_001_(paired)_150721_contig_1   2   p1  (A)11   11  2102    2112  P_S1_L001_R1_001_1_(paired)_150727_contig_10  1   p1  (A)10   10  5047    5056

I tried to use the hash in perl but it is not working.

    open(src,"@ARGV[0]");
while($line = <src>)
{

chomp($line);
@a = split(/\t/,$line);
$key = shift(@a);
$value = join("\t",@a);
$hash{$key} = $value;

}

close(src);


    open(FILE,"@ARGV[1]");
    while($line1 = <FILE>)
    {

    chomp($line1);
    @b = split(/\t/,$line1);
    $key1 = shift(@b);
    $value1 = join("\t",@b);

        if(exists $hash{$key1})
        {

        print"$key1\t$hash{$key1}\t$key1\t$value1\n";       

        }   

    }
ssrs rna-seq misa python perl • 181 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by kartikayprasad10
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