Hi,

First, your DNA sequences are less than 15 character long. I'll assume it is just a mistake in your example, but this may need further clarification.

Assuming that you want to:

- omit lines starting with ">" (headers);

- remove lines more than 30 or less than 15 characters, and

- count the number of occurrences of each individual sequence,

you could do something like this: 

use strict;
use warnings;

my %count_seq;
while (<DATA>) { 
    chomp;
    next if /^>/;     # discard headers
    next if length($_) > 30 or length($_) < 15; # discard unwanted siz
+es
    $count_seq{$_}++;   # count occurrences
}
print "$_\t$count_seq{$_}\n" for keys %count_seq;

__DATA__
>dfbdbgf_356dfbdf
ATGGCTGGATATCGATT
>sdgthhr_478364df
ATGGCTATGGATCAGATT
>dfbdbgf_356dfbdf
ATGGCTATCGATT
>dfbdbgf_356dfbdg
ATGGCTGGATATCGATT
>sdgthhr_478364df
ATGGCTATGGATCGATT
>dfbdbgf_356dfbdg
ATGGCTGGATATCGATT
>sdgthhr_478364df
ATGGCTATGGATCGATT
TGCATGCGCTATTAGCG
ATGGCTATGGATCGATT
TGCATGCGCTATTAGCG
ATGGCTATGGATCGATT
TGCATGCCCTATTAGCG

[download]
This gives me the following result: 
$ perl dna_seq.pl
TGCATGCGCTATTAGCG       2
ATGGCTATGGATCAGATT      1
ATGGCTGGATATCGATT       3
ATGGCTATGGATCGATT       4
TGCATGCCCTATTAGCG       1

[download]

In reply to Re: How to format fasta file by Laurent_R
in thread How to format fasta file by andyBio

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