Get bounds for all regions: CDRs and FWRs

[nbst...@gmail.com]

Is there a way to get bounds for all the regions: FWR1, CDR1, FWR2, CDR2, FWR3, CDR3, FWR4? Or are we left to our own devices for this. After doing:

utils.process_input_line(line)
utils.add_implicit_info(glfo, line)

I didn't see any info in the 'line' variable from which the boundaries of these regions could be determined (with the exception of CDR3). I suppose FWR4 is trivial. Happy to write some code to figure this out myself, but figured I'd ask to see if there is a way to do it within the code you have here. Thanks!

-Nicolas

[Jakub Otwinowski]

I was able to pass data to mixcr which is capable of identifying all of these quite easily. 

Jakub

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[Duncan Ralph]

Passing to mixcr is probably a good way to go. You can also use the --presto-output, which'll output things in imgt-aligned form, but then you have to supply imgt-aligned germline files (i.e. cat together the V D and J fastas downloaded from here http://www.imgt.org/vquest/refseqh.html).

The trouble is that while the CDR3 is pretty unambiguously defined, the other ones are a bit more subjective. There was a thread on b-t.cr about this, but I'm not seeing it now. In any case, as a practical matter, I can define the cdr3 pretty unambiguosly with cyst/tryp/phen that are pretty reliably aligned, but specifying the other CDR/FWK relies on a particular alignment choice, probably imgt, and they're always changing things so I don't want to depend on it.

On Thu, Nov 30, 2017 at 1:59 PM, Jakub Otwinowski <jak...@sas.upenn.edu> wrote:

I was able to pass data to mixcr which is capable of identifying all of these quite easily. 

Jakub

On Thu, Nov 30, 2017 at 4:34 PM <nbst...@gmail.com> wrote:

Is there a way to get bounds for all the regions: FWR1, CDR1, FWR2, CDR2, FWR3, CDR3, FWR4? Or are we left to our own devices for this. After doing:

utils.process_input_line(line)
utils.add_implicit_info(glfo, line)

I didn't see any info in the 'line' variable from which the boundaries of these regions could be determined (with the exception of CDR3). I suppose FWR4 is trivial. Happy to write some code to figure this out myself, but figured I'd ask to see if there is a way to do it within the code you have here. Thanks!

-Nicolas

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[Nicolas Strauli]

Yeah I was just reading the b-t.cr thread ( https://b-t.cr/t/standardizing-the-format-of-a-germline-set/143/26 ). I thought it would be way easier. Like a simple regular expression or something. I guess not. I'll try mixcr.

[Duncan Ralph]

Here's an old email from someone with details on the --presto-output and some attached aligned germline files. (with crappy formatting, sorry).

Hi Davide,

Presto output is in terms of the official IMGT V alignments, which I don't keep track of anywhere in partis, partly because they seem to change, so I decided it made more sense to make people use their own so they were sure they were using the one they wanted. But, yes! I should've actually explained what it is.

So basically they're the aligned fastas from here, but I've attached ones that I think should work if you're not particular about imgt versions.

lmk if that doesn't work.

On Tue, Oct 24, 2017 at 8:12 AM, Davide Bagnara <davide....@edu.unige.it> wrote:
Hi Duncan,

I am trying to get partis work with  --presto-output, but I don’t understand what do you mean with this:

 --aligned-germline-fname ALIGNED_GERMLINE_FNAME
                        fasta file with alignments for each V gene (default: None)

Could you send me an example?

Thanks,
Davide

On Thu, Nov 30, 2017 at 2:25 PM, Duncan Ralph <dkr...@gmail.com> wrote: