Issue of using pair-end WES data

Dear developer, 

I noticed that pyIR currently supports input in the form of a single FASTA/FASTQ file. I'm working with paired-end Whole Exome Sequencing (WES) data and was wondering about the best approach to use this data with pyIR. Should I preprocess the paired-end data into a single file using tools like pRESTO before inputting it into pyIR?

Thanks for your guidance!