I have to calculate the Shannon entropy for a given list of sequences in a fasta file. Recently I came across a program called rnaentropy which solves my problem but the issue is I cannot run sequences in batch. In the documentation the input is given as a sequence of strings. The parameters in the documentation is as follows:
<pre>
./RNAentropy "sequence" -s sequence -t temperature -e energyModel(default 2004) -d delta_Temp (compute structural entropy using  &lt;E> = RT² * d/dT ln(Z(T)) ) -c (centered) -z energy_is_zero [0|1] (default 0)  -v (verbose, extended output)
       ./RNAentropy -h (detailed help)  

Input paramters are:
   &lt;sequence>          :  If FIRST argument is a valid nucleotide sequence it will be used input
   -s  &lt;sequence>      : Alternative flag for input sequence
   -t  &lt;temperature>   : Temperature in ºC (default is 17ºC)
   -e  &lt;energy_model>  : Thermodynamic energy model used. Valid values for energy model are 1999, 2004 and 2007 (resp. Turner'99, Turner'04 and Andronescu '07) (default is 2004)
   -d  &lt;delta_T>       : Temperature variation used for estimating d/dT ln(Z(T))
                        NOTE: If this parameter is provided, H is computed estimating  &lt;E> = RT² * d/dT ln(Z(T))
   -c                 : (Use only in combination of -d) Use the centered version for estimating  &lt;E> = RT² * d/dT ln(Z(T)) 
   -v                 : Output includes method for computing H and the name of the ouput parameters
   -z  &lt;energy_is_zero>: [0|1] If value is 1, energies are set to 0, ouput is structural entropy for the uniform case 
</pre>

Can anyone please suggest me a way to do it for a multi-fasta? Is there a way to iterate in a shell script? 
I wouuld use a Perl (or Python script) to parse the multifasta and run your tool, like:

    #!/usr/bin/perl
    
    use strict;
    use warnings;
    
    $/="\n>"; # read fasta sequences in blocks
    while (<>) {
         s/>//g;
         my ($id, @seq) = split (/\n/, $_);
         my $seq = join "", @seq; # rebuild the sequence, one single line
         print "$id\n"; # to indicate which sequence is being analyzed
         system("./RNAentropy -s $seq"); # run the command, add params if needed
    }


then you can run as `perl analyzeSeq.pl < multifasta_in > output_file`