GTF from consensus sequence
"Transforming" Fasta files to GTF or GFF3 files is a common request, as are similar tasks such as "converting" BAM files to VCF files. But these are underdefined questions, and "transform" or "convert" isn't really the right way to think about the task.

As far as your particular request is concerned, Fasta files and GTF files contain fundamentally different types data.


Fasta files contain sequences, which could be chromosomes, assembled contigs, polypeptides, transcripts, or other biological sequences.
GTF (and GFF3 and BED) files contain intervals, indicating that some feature of interest occurs at such-and-such position on such-and-such sequence. A hypothetical example: a transcription factor binding site occurs on chromosome 2 from position 40011 to 40017.


So you are correct: it's not really helpful to think of your task in terms of "transforming" Fasta to GTF. The process of creating a GTF/GFF3/BED file is often called annotation. There are many different methods to annotate many different types of genomic features: transposable elements, segmental duplications, protein-coding genes, non-coding RNAs, and so on.

As a result, it's meaningless to say "I need a GTF file" without clearly specifying what that GTF file will annotate. (It's kind of like saying "I need an XML file" or "I need an Excel spreadsheet" without indicating what the contents of those files would be.) The things you need to clarify are:


What will the intervals in my GTF file represent?
What precise sequences will serve as the reference and provide interval coordinates for the GTF file?
How are those intervals to be determined?


It sounds like 3. is a big part of your question. If I'm reading things correctly, you want to annotate a particular class of genes on an influenza genome. Is that correct? Did you perform de novo sequencing of influenza viruses, and now hope to characterize variation in their HA genes? Stating what you hope to get out of your analysis would be helpful in finding a good way forward.