This is a very simple script to create a batch file to analyze multiple peptide sequences parallely with EMBOSS.
Just save your .FASTA files in a folder named fastaseq and execute the script with perl:
perl protein_analyzer.pl
Then you have to call the BATCH file generated (emboss.bat) to execute the EMBOSS comands.
In the documentation it is attached a .bat example file to analyze the sequence of protein PDL-1, also attached as Q9NZQ7.fasta. You can see the analysis results in the DATA folder.
You can also see the HMMER Analysis result in HMMER_DATA folder.