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:
./RNAentropy "sequence" -s sequence -t temperature -e energyModel(default 2004) -d delta_Temp (compute structural entropy using <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: <sequence> : If FIRST argument is a valid nucleotide sequence it will be used input -s <sequence> : Alternative flag for input sequence -t <temperature> : Temperature in ºC (default is 17ºC) -e <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 <delta_T> : Temperature variation used for estimating d/dT ln(Z(T)) NOTE: If this parameter is provided, H is computed estimating <E> = RT² * d/dT ln(Z(T)) -c : (Use only in combination of -d) Use the centered version for estimating <E> = RT² * d/dT ln(Z(T)) -v : Output includes method for computing H and the name of the ouput parameters -z <energy_is_zero>: [0|1] If value is 1, energies are set to 0, ouput is structural entropy for the uniform case
Can anyone please suggest me a way to do it for a multi-fasta? Is there a way to iterate in a shell script?