open (FH, "p.txt"); while ($seq=) { @seq = split /\t/, $seq; print @seq[0]."\t"; opendir(DIR, "."); @files = grep(/\.fq$/,readdir(DIR)); closedir(DIR); foreach $file (@files) { @file1 = split /\./, $file; $file2 = $file1[0]; $size = @files; $file3 = $file2."\t".$file3;} for ($i = 1; $i <= $size; $i++) { @seq1 = split /\./, @seq[$i]; chomp @seq1[0]; if (@seq1[0] eq $file2) {print "1"."\t";} else {print "0"."\t";} } print "\n"; }