loading protein SAM into Jalview


Is it possible to load a SAM file produced by ncbi-blastp into Jalview, so that it displays all the hits against a reference sequence similarly to a samtools tview pileup?

Thanks in advance,

Hi Albert! Good to hear from you!

We have a branch waiting in the wings where we experimented with bam import which should work for protein sam. If it’s urgently needed I can quickly check to see if it will play nice with our current development branch so you can try it out ?

Couldn’t resist the temptation over morning coffee.

The bam import mechanism is barely usable since it needs to know what range of the reference you are interested in importing, and dies horribly if that range isn’t present. It does work, despite some failing tests !

I had a quick look at NCBI Blast’s ‘SAM’ output format - it looks like it is simply borrowing SAM’s flavour of CIGAR, so there’s a good chance htsjdk won’t handle it. Can you post a sample of the output you’d like to parse ?

The ncbi web site has a SAM output, guess that’s what you mean ? I’ve also discovered file attachments tbat dont look like images don’t seem to be supported on the forum… we will see what we can do about that.

I’ve hacked @kmourao’s working prototype of BAM import so it works for plain SAM @albert_vilella. It still needs a region spec, for now, and isn’t clever enough to infer the reference sequence (is that even in the blast output ?).

Issue is here:
Executable jars of the prototype build for java 11 and 8 are at:
( make sure they are dated at least after 6pm uk time 1st Oct !)

There may be broken things :crazy_face: @ben_soares might be able to take this on next week and deal with them whilst I’m otherwise engaged.