I have files with hundreds of sequences with frequency values reported as "Freq X" and missing characters represented by a dash ("-"), something like this
I need to scan each sequence and if a dash is found, it must be replaced with the character that is present at >80% in that particular position. In the example above, the dash in the second sequence located in the second position should be replaced by a "T", since "T" is found in 700 sequences according to the Freq value. Then, the dash in the last sequence should be replaced by an "A", since the frequency of "A" is 700 representing >80% of the total sequences.
The expected output should be something like this:
$ awk '/>/{fr=$3;getline;n=split ($0,a,""); for (i=1;i<=n;i++) b[i"-"a[i]]+=fr}\
END{for (i in b) {split (i,c,"-"); if (d[c[1]]<=b[i]){e[c[1]]=c[2];d[c[1]]=b[i]}}\
for (i in e) print i" "e[i]}' Input | awk 'NR==FNR{a[$1]=$2;next}\
{n=split($0,b,"");for (i=1;i<=n;i++) if (b[i]=="-") b[i]=a[i]; for (i=1;i<=n;i++) printf b[i];\
printf "\n"}' - Input
The problem is that this code will replace for the majority regardless of the 80% rule
Any help will be greatly appreciated
Moderator's Comments:
Please use CODE tags (not QUOTE, FONT, and COLOR tags), to display sample input, sample output, and code segments.
Last edited by Xterra; 06-20-2015 at 11:35 AM..
Reason: Fix tags.
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06-19-2015
