CcLG01 22 + CHH 0.200 5.00 1 5 0 0 0.036 0.624 CcLG01 23 + CHH 1.000 1.00 1 1 0 0 0.207 1.000 CcLG01 28 + CHH 0.200 5.00 1 5 0 0 0.036 0.624 CcLG01 29 + CHH 1.000 1.00 1 1 0 0 0.207 1.000 CcLG01 30 + CHH 1.000 1.00 1 1 0 0 0.207 1.000 CcLG01 33 + CHH 0.250 4.00 1 4 0 0 0.046 0.699 CcLG01 39 - CHH 0.500 2.00 1 2 2 2 0.095 0.905 CcLG01 42 - CHH 0.000 2.00 0 2 1 1 0.000 0.658 CcLG01 49 + CHH 0.000 1.00 0 1 3 3 0.000 0.793 CcLG01 60 - CHH 0.000 3.00 0 3 1 1 0.000 0.562 CcLG01 61 + CHH 0.000 1.00 0 1 3 3 0.000 0.793 CcLG01 62 + CHH 0.000 1.00 0 1 3 3 0.000 0.793 CcLG01 72 - CHH 0.000 4.00 0 4 1 1 0.000 0.490 CcLG01 75 - CHH 0.000 4.00 0 4 0 0 0.000 0.490 CcLG01 80 - CHH 0.000 4.00 0 4 0 0 0.000 0.490 CcLG01 94 - CHH 0.000 4.00 0 4 0 0 0.000 0.490 CcLG01 97 - CHH 0.000 4.00 0 4 0 0 0.000 0.490 CcLG01 99 - CHH 0.000 4.00 0 4 0 0 0.000 0.490 CcLG01 116 - CHH 0.000 2.00 0 2 0 0 0.000 0.658 CcLG01 126 - CHH 0.000 1.00 0 1 0 0 0.000 0.793 CcLG01 133 - CHH 0.000 1.00 0 1 0 0 0.000 0.793 CcLG01 199 - CHH 0.000 1.00 0 1 0 0 0.000 0.793

Blockquote

i think you want to find the bin,that have at least 3 methylation cytosines in each 100bp bin? so perl exmaple:

while (<IN>) {

 chomp;

  my @tmp = split;

  $flag = int($tmp[1]/100)+1;

  if ($tmp[6] == 1) {

    push @db{$flag},"$tmp[1]";

  }

}

print "#flag\tstart\tend\tnumber of methylation\tmethylation positon\n"; 

foreach my $k (sort{$a<=>$b} keys %db) {

  my $s = ($k-1)*100+1;

  my $e = $k*100;

  my $num = scalar(@{$db{$k}});

  print "$k\t$s\t$e\t$num\t",join(",",@{db{$k}}),"\n";

}

you can filter the result by youself!!!!

You can use grep() function to find the indexes of one chr.

data<-read.table("PATH",
                 header=F,
                 sep="\t",
                 )
chr<-as.character(levels(data[,1]))
bin<-function(chr){
  index<-grep(chr,data[,1])
  start<-data[index[1],2]
  end<-data[index[length(index)],2]
  position<-start-end
  cytosine<-sum(data[index,7])
  coverage<-sum(data[index,8])
  if(position>100 & cytosine>3){
    return(c(chr,start,end,cytosine,coverage))
  }
}
result<-t(apply(matrix(chr,ncol=1),1,bin))
colnames(result)<-c("chr","shart","end","cytosine","coverage")

The result is :

> result
     chr      shart end  cytosine coverage
[1,] "CcLG01" "22" "199" "7"      "56"

And you can output:

write.table(result,"PATH",col.names = T,row.names = F,sep="\t",quote=F)

Dear zjhzwang, when i used " result<-t(apply(matrix(chr,ncol=1),1,bin))" command..i got error.

data=read.table("Sterile_05.txt", header=F, sep="\t")
> chr<-as.character(levels(data[,1]))
> bin<-function(chr){
+   index<-grep(chr,data[,1])
+   start<-data[index[1],2]
+   end<-data[index[length(index)],2]
+   position<-start-end
+   cytosine<-sum(data[index,7])
+   coverage<-sum(data[index,8])
+   if(position>100 & cytosine>3){
+     return(c(chr,start,end,cytosine,coverage))
+   }
+ }

> result<-t(apply(matrix(chr,ncol=1),1,bin))
Error in t.default(apply(matrix(chr, ncol = 1), 1, bin)) : 
  argument is not a matrix
> result<-apply(matrix(chr,ncol=1),1,bin))
Error: unexpected ')' in "result<-apply(matrix(chr,ncol=1),1,bin))"
> result<-apply(matrix(chr,ncol=1),1,bin)
> result
NULL

Dear zjhzwang

One more question i want to add column 7 based on the column 2. But the addition should be based on a another file which have start and end position

like I have a another file in this format chr start end CcLG01 1 45

So from position 1 to 45 in another file (previous, mentioned above) column 7 should be added.

Thank You