Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Alphabet counting

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Alphabet counting
# 1  
Old 01-26-2012
Alphabet counting
I have a text file in the following format
Code:
CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT

Each row/line will have 32 letters and each line will only have multiple occurrences of 2 letters out of a pool of ATGC (also small atgc). some may have also '-'. I would like to count the occurrence of each alphabet in a line and output the position number/ numbers of the smallest counted alphabet.

Code:
CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC  G 7
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA   T 5
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT  G 2 15 16
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT    C 15

Please let me know the best way to do it using awk.
Thanks
# 2  
Old 01-26-2012
Have a go with this:

Code:
awk '
    {
        n = split( $0, a, "" );
        for( i = 1; i <= n; i++ )
        {
            count[a[i]]++;
            pos[a[i]] = sprintf( "%s%d ", pos[a[i]], i );
        }

        min = "";
        for( x in count )
        {
            if( match( x, "[ACGT]" ) && (min == "" || count[x] < count[min] ) )
                min = x;
        }

        print $0, min, pos[min];

        delete count;
        delete pos;
    }
' input-file >output-file

Last edited by agama; 01-26-2012 at 11:28 PM.. Reason: better form
This User Gave Thanks to agama For This Post:
Lucky Ali
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Shell Script - Alphabet in code

Hi e Hi everyone, I can't make this script work, #! /bin/bash declare -A crypt=( ="A" ="a" ="B" ="b" ="C" ="c" =' ' ='!' ) encode () { local word=$1 for ((i=0; i<${#word}; ++i)) ; do local char=${word:$i:1} printf %s' ' ${crypt} done ... (5 Replies)
Discussion started by: Pinguino
5 Replies

2. Shell Programming and Scripting

Conditional for every letter in alphabet

I wanted to know if there was a more efficient to do this. I was to setup a conditional for every letter of the alphabet, like so (I am parsing an array): for i in "${arr}"; do if ]; then echo "$i starts with A" else echo "$i does not start with A" fi done I want to do this A-Z, is there... (6 Replies)
Discussion started by: sudo
6 Replies

3. Shell Programming and Scripting

Help with sort alphabet on specific column

Input file: POL B7U6K8 Avian_reticuloendotheliosis_virus POLB B7Z1W5 Homo_sapiens POLB H9G5Y0 Anolis_carolinensis POLD1 Q642R8 Xenopus_laevis POLD2 H0YZC7 Taeniopygia_guttata POLD3 F1P540 Gallus_gallus POLDIP3 Q5F4B6 Gallus_gallus POLE2 E1C2T8 Gallus_gallus... (3 Replies)
Discussion started by: perl_beginner
3 Replies

4. Shell Programming and Scripting

Recode alphabet into numbers

I have a genotype.bim file where it contains information about SNPs and genotype. As a hypothetical example, let's say genotype.bim snp1 ... A G snp2 ... G T snp3 ... G T snp4 ... G A ... snpN ... C G where first column identifies each SNP and 5th and 6th column has genotype... (3 Replies)
Discussion started by: johnkim0806
3 Replies

5. Shell Programming and Scripting

last character is digit or alphabet!

Hello, I have to find out whether the last character is digit or alphabet. I manage to strip the last character but would need some help if there is one liner available to test the above. set x = WM echo $x | sed 's/.*\(.$\)/\1/' O/P M I would like a one liner code to test whether the... (1 Reply)
Discussion started by: dixits
1 Replies

6. UNIX for Dummies Questions & Answers

poly to mono alphabet for every 2nd line

Hi, Can anyone teach me by using perl. let say i have an input file that content like below: ->line_01 aaabbbDDDTTTUSSy ->line_02 cccdddEEESSSGTTT ->line_03 xxxxyyyyzzzzzzzzzz want the above input file content to become output file like below (every 2nd line after ->... become mono... (0 Replies)
Discussion started by: eisya10
0 Replies

7. UNIX for Dummies Questions & Answers

checking wether an input is using letters of the alphabet

afternoon forums. I need to get a way of testing as to wether an inputed character is part of the english alphabet. i have come up with the following code but its not working at all. until '] do echo This is not a Letter done any help would be beneficial to me. (1 Reply)
Discussion started by: strasner
1 Replies

8. Shell Programming and Scripting

To check if the first character is a alphabet or number

Hi, I need to find whether the first character in a line is a alphabet or a number. If its a number i should sort it numerically. If its a alphabet i should sort it based on the ASCII value.And if it is something other than alphabet or number then sort it based on ASCII value. The code i used... (2 Replies)
Discussion started by: ragavhere
2 Replies

9. Programming

output the letters of the alphabet with the number of occurrences

hi, I'm trying to create a program that will read a file and then check the file for each letter of the alphabet and then output the letter and the number of times it appears in the file, into a new file... this is what i have so far but it's not working.. if anyone could help that would be nice!... (10 Replies)
Discussion started by: svd
10 Replies

10. Shell Programming and Scripting

What can i do to check that the input is all alphabet.. ?

What can i do to check that the input is all alphabet.. ? (4 Replies)
Discussion started by: XXXXXXXXXX
4 Replies
Login or Register to Ask a Question