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Filtering my major and minor values

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Top Forums Shell Programming and Scripting Filtering my major and minor values
# 1  
Old 01-03-2013
Filtering my major and minor values
I want to remove all rows with a minor repeating count less than 30% compared to the major repeating count from my table. The values of a col(starting col 2) can assume is A,T,G,C and N. Each row has at least 2 values and at most 4 repeating values(out of ATGC).
N is considered a missing value and shouldn't be considered.

These are the rules for filtering.

Consider the row which has a count of 4 for Ts and 1 for As (starting col 2).
S10_14113025 T T T A T
If the count of the minor repeating value is less than 30% of the major repeating value, delete the row.

So count(A)/count(T)=1/4=25% < 30%...this row should be removed.

Consider the row with 2 Ts, and 1 A.
S10_14113025 T N N A T
Ignoring the Ns, the minor frequency is
count(A)/count(T)=1/2=50% > 30% ....this row should NOT be removed.

Consider the row with more than 2 values (3 in this case as in G,C,A).
S10_14113072 G C A G N
this row should NOT be removed,nothing needs to be calculated.


Inp

Code:
S10_14113025        T    T    T    A    T    T
S10_14113072        A    C    C    A    A    A
S10_14113073        G    C    G    G    C    N
S10_14113079        G    C    C    C    N    N
S10_14113080        G    C    C    C    N    A
S10_14113027        T    T    N    A    N    N

desired out

Code:
S10_14113072        A    C    C    A    A    A
S10_14113073        G    C    G    G    C   N
S10_14113080        G    C    C    C    N    A
S10_14113027        T    T    N    A    N    N

# 2  
Old 01-03-2013
given your explanation - I don't understand the LAST example. Why "nothing needs to be calculated"?
Are you only considering As and Ts?
This User Gave Thanks to vgersh99 For This Post:
newbie83
# 3  
Old 01-03-2013
We only need to filter rows having biallelic nature (exactly two values excluding N).
The rows with more than two values are biologically significant and cant be filtered out.
# 4  
Old 01-03-2013
ok, I almost got it, but....
why exactly this line did NOT make it into the output?
Code:
S10_14113079        G    C    C    C    N    N

This User Gave Thanks to vgersh99 For This Post:
newbie83
# 5  
Old 01-03-2013
it's a bit verbose, but can be used as a start.
awk -f newbie.awk myInputFile
newbie.awk:
Code:
function initVars()
{
  split("",n)
  split("",a)
  c=0
}

{
  for(i=2;i<=NF;i++)
    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()
}

# 6  
Old 01-03-2013
I`m sorry that line should be included...my bad Smilie
# 7  
Old 01-03-2013
Quote:
Originally Posted by newbie83
I`m sorry that line should be included...my bad Smilie
then try the suggestion
This User Gave Thanks to vgersh99 For This Post:
newbie83
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