sequence_locator: alignment error and additional outputs

[ArtPoon]

I ran the following query:

art@Wernstrom poplars % python3 poplars/sequence_locator.py locate hiv NA ggacgaaagaaagccagagagtctctcgacgcaggactcggcttgctgaagg  

Regions touched by query1

Alignment of the query sequence to HXB2
	Query	 ggacgaaagaaagccagagag--tctctcgacgcaggactcggcttgctgaagg	52
	         .*  .**.*.**.******..  ****************************** 
	Ref  	 agcgaaagggaaaccagaggagctctctcgacgcaggactcggcttgctgaagc	712

The same query gave me the following result with LANL:

 Query GGACGAAAGA -AAGCCAGAG -AG-TCTCTC GACGCAGGAC TCGGCTTGCT  47
          ::::::   :: ::::::  :: :::::: :::::::::: :::::::::: 
  HXB2 AAGCGAAAGG GAAACCAGAG GAGCTCTCTC GACGCAGGAC TCGGCTTGCT  707

 Query GAAGG  52
       ::::      
  HXB2 GAAGC  712

which also returns the following useful information:

[kwade4]

Thanks for catching that bug! Sorry about that! I will definitely have a look. It's supposed to print the same output as LANL (i.e. a table with the same headings). I suspect that the output isn't printing because of an indexing error.

I'm surprised that the alignment is incorrect - I use MAFFT to align the query and reference sequence.

[ArtPoon]

It's not that the alignment is incorrect - there isn't a clean alignment in either case, although there are probably different gap penalties being used. The issue is more about the missing output. Thanks!