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? 
With GNU Parallel (https://www.biostars.org/p/63816/) you would do:

    cat in.fasta |
      parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")'     


From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutorial.html#Informational):
>  `--recend str`    Record end separator for `--pipe`.   
>  `--recstart str`  Record start separator for `--pipe`.