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Shell Programming and Scripting

Filtering my major and minor values

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Top Forums Shell Programming and Scripting Filtering my major and minor values
# 8  
Old 01-03-2013
try also:
Code:
awk '
{
  delete a; mx=0; mn=100;
  for (i=2; i<=NF; i++) a[$i]++;
  for (i in a) {
    if (a[i] > mx ) mx=a[i];
    if (a[i] < mn ) mn=a[i];
  }
}
(mn / mx) * 100 > 30
' input

# 9  
Old 01-03-2013
Quote:
Originally Posted by rdrtx1
try also:
Code:
awk '
{
  delete a; mx=0; mn=100;
  for (i=2; i<=NF; i++) a[$i]++;
  for (i in a) {
    if (a[i] > mx ) mx=a[i];
    if (a[i] < mn ) mn=a[i];
  }
}
(mn / mx) * 100 > 30
' input

good idea, but.... a couple of missing points:
  1. you're counting Ns as legit fields while they should be skipped
  2. there's no provision to print lines with more than 2 unique field values
  3. 'delete a' doesn't work on all awk-s. Most awk's don't allow deleting the whole array that way, but only individual array entries. Therefore, the trick is to use 'split' to null-out the array in one step.
# 10  
Old 01-04-2013
Hi,

There is one more filter that needs to be considered.
I want to treat any character other than A,C,G,T,N as a missing value N.
In the example, the character Y is treated as if it was a missing value N since it
does not belong to the subset {A,C,G,T,N}.

For example the row
Code:
S10_14113072        A    C    C    A    A    Y

needs to be treated the same as
Code:
S10_14113072        A    C    C    A    A    N

But if such a row appears in the output it should appear as
Code:
S10_14113072        A    C    C    A    A    Y

---------- Post updated at 06:02 PM ---------- Previous update was at 05:57 PM ----------

I have done a small modification
Code:
if ($i != "[ACGTN]") { $i = "N" }

Doesnt seem to work. please help me with the correct code?


Code:
function initVars()
{
  split("",n)
  split("",a)
  c=0
}

{
  for(i=2;i<=NF;i++)
    if ($i != "[ACGTN]") { $i = "N" } 
    if ($i != "N") {
     if (!($i in a))
       n[++c]=$i
     a[$i]++
    }

  if (c>2) { initVars(); print;next }

  div=a[n[1]]/a[n[2]]
  div=(div>1)?1/div:div
  if ( div*100 > 30)
     print
  initVars()
}

Last edited by newbie83; 01-04-2013 at 06:18 PM..
# 11  
Old 01-04-2013
Change
Code:
  for(i=2;i<=NF;i++)
    if ($i != "[ACGTN]") { $i = "N" } 
    if ($i != "N") {
     if (!($i in a))
       n[++c]=$i
     a[$i]++
    }

to
Code:
  for(i=2;i<=NF;i++)
    if ($i ~ /[ACGT]/) {
     if (!($i in a))
       n[++c]=$i
     a[$i]++
    }

# 12  
Old 01-05-2013
awk
Code:
awk '{
    l_max=l_min=hasN=cnt=0
    delete _
    for(i=2;i<=NF;i++){
        if($i=="N")
            hasN=1
        _[$i]++
    }
    for(i in _){
        cnt++
        if(l_max==0 || _[i]>=l_max)
            l_max=_[i]
        if(l_min==0 || _[i]<=l_min)
            l_min=_[i]
    }
    if((cnt==2 && hasN==0) || (cnt==3 && hasN==1)){
        per=l_min/l_max
        if(per>=0.3)
            print $0
    }
}' yourfile

# 13  
Old 01-05-2013
change
Code:
if ($i != "N") {

to
Code:
if ($i != "N" && $i ~ /[ACGT]/ {
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