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Shell Programming and Scripting

Data counting

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# 1  
Old 01-26-2012
Data counting
I have a large tab delimited text file with 10 columns
for example
Code:
chrM  412  A  A  75   0  25  2     ..,AGAATt       II
chrM  413  G  G  72   0  25  4     ..t,,Aag     IIIH
chrM  414  C  C  75   0  25  4     ...a,..     III2
chrM  415  C  T  75  75  25  4     TTTt,,,ATC     III7

At column 9, I want to count the occurrence of each of the character. The characters I need to count for each line is .(point) , (comma), A/a, T/t, C/c, G/c.

So that I could get a file as below.
Code:
value at column 2  Count of "."  Count of ","   Count of "A/a"  Count of "G/g"   Count of "C/c"  Count of "T/t" 
412                         2              1                       3                   1                     0                   2
413                          2              2                       2                  1                     0                   1
414 
415
...
....
.....
for all the numbers in column 2 of the input file

Please let me know the best way to do this using awk or sed.
# 2  
Old 01-26-2012
Try:
Code:
perl -anle '$,=" ";print $F[1],map {$_?$_:"0"}($F[8]=~s/\.//g,$F[8]=~s/,//g,$F[8]=~s/a//ig,$F[8]=~s/g//ig,$F[8]=~s/c//ig,$F[8]=~s/t//ig)' file

Shorter:
Code:
perl -anle '$,=" ";$_=$F[8];print $F[1],map {$_?$_:"0"}(s/\.//g,s/,//g,s/a//ig,s/g//ig,s/c//ig,s/t//ig)' file

Last edited by bartus11; 01-26-2012 at 07:40 PM..
# 3  
Old 01-26-2012
Try this: (in Awk)

Code:
awk '{d=gsub("[.]","",$9);a=gsub("[Aa]","",$9);g=gsub("[Gg]","",$9);c=gsub("[Cc]","",$9);Co=gsub("[,]","",$9);t=gsub("[Tt]","",$9); print $2" "d " "a" "g" "c" "Co" "t }' file

# 4  
Old 01-26-2012
Something similar...
Code:
awk 'BEGIN{
        l=split(". , A G C T",arr," ")
        printf "Column 2 ";
        for(i=1;i<=l;i++)
                printf("Count of \"%s/%s\" ", arr[i], tolower(arr[i]))
        printf("\n")
        
}
{
        c=gsub(/\./,"",$9); printf("%-9s%-15s",$2,c);
        for(i=2;i<=l;i++){
                x=$9;c=gsub(arr[i],"",x);
                c+=gsub(tolower(arr[i]),"",x)
                printf("%-15s", c)
        } printf("\n") 
}'  infile

If you have more characters, just append it to the array in the BEGIN block.

--ahamed
Last edited by ahamed101; 01-26-2012 at 08:20 PM..
# 5  
Old 01-27-2012
Code:
awk 'BEGIN{print "Value\t.\t,\tA/a\tG/g\tC/c\tT/t"}
    { s=tolower($9);l=split(s,a,"");
      for (i=1;i<=l;i++) b[a[i]]++;
      print $2,b["."]+0,b[","]+0,b["a"]+0,b["g"]+0,b["c"]+0,b["t"]+0;
      delete a;delete b}' OFS="\t" infile

Value   .       ,       A/a     G/g     C/c     T/t
412     2       1       3       1       0       2
413     2       2       2       1       0       1
414     5       1       1       0       0       0
415     0       3       1       0       1       5

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