cdr3 boundaries

[Jakub Otwinowski]

I want to get the cdr3 boundaries. The code has changed, so what is now the easiest way to spit out the boundaries in the annotation csv?

Jakub

[Duncan Ralph]

This should do it, modulo pseudocodery (also attached, but not sure how google groups will handle that):

import csv
import sys
partis_path = '.'
sys.path.insert(1, partis_path + '/python')
import utils
import glutils

glfo = glutils.read_glfo(partis_path + '/data/germlines/human', chain='h')

with open(partis_path + '/test/reference-results/annotate-new-simu.csv') as csvfile:
    reader = csv.DictReader(csvfile)
    for line in reader:
        utils.process_input_line(line)
        utils.add_implicit_info(glfo, line, existing_implicit_keys=('aligned_d_seqs', 'aligned_j_seqs', 'aligned_v_seqs', 'cdr3_length', 'naive_seq', 'in_frames', 'mutated_invariants', 'stops', 'mut_freqs'))
        utils.print_reco_event(glfo['seqs'], line)
        cdr3_bounds = (line['codon_positions']['v'], line['codon_positions']['j'] + 3)
        print ''
        print 'should match the above:'
        print '%s naive cdr3' % line['naive_seq'][cdr3_bounds[0] : cdr3_bounds[1]]
        print '%s mature' % line['seqs'][0][cdr3_bounds[0] : cdr3_bounds[1]]
        break

On Mon, Nov 7, 2016 at 12:40 PM, Jakub Otwinowski <jak...@sas.upenn.edu> wrote:

I want to get the cdr3 boundaries. The code has changed, so what is now the easiest way to spit out the boundaries in the annotation csv?

Jakub

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[Jakub Otwinowski]

Thanks, it mostly works, except it eventually hits this error

Traceback (most recent call last):

  File "<stdin>", line 5, in <module>

  File "/partis/python/utils.py", line 822, in add_implicit_info

    uneroded_gl_seq = glfo['seqs'][region][line[region + '_gene']]

KeyError: ''

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[Duncan Ralph]

yeah, that'll be a failed sequence, presumably you want to skip it.

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[Duncan Ralph]

Removed the necessity for the crappy implicit key argument, and added this script to github:

https://github.com/psathyrella/partis/blob/master/bin/example-output-processing.py

[halas...@gmail.com]

Hi,

Is there a version to get the CDR3 boundaries (i.e. where the Vends, the N starts and ends, etc etc.) for TCR sequences?

Hussein

[Duncan Ralph]

An old version of the example actually has how to access the cdr3 boundaries in it. Let me know if it isn't clear.

a couple notes:

  - cdr3 boundaries and V/N boundaries aren't the same -- if you want the latter, which I call regional bounds, they're stored in the same dict with the key 'regional_bounds', as a (start, end) pair for each region (v, d, j) that's zero-indexed and python-slice-conventioned.

  - there's nothing different about how to access this for TCRs, although as you've probably already worked out you need to specify the --locus on the command line

  - and... I just realized last week that I screwed up my cdr3 length nomenclature! The numbers I point you to above ^ are fine, since all my codon positions are fine. But, imgt calls the "cdr3 length" the length *excluding* the six bases in the codons, while "junction length" *includes* them, and I somehow reversed this at some point. When I finish freaking out about this and figure out how to fix it without confusing backwards compatibility breakage I'll send a mail to the list.

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[Duncan Ralph]

I just added an option --extra-annotation-columns so you can specify non-default annotation columns to write to the annotation output file. So, for instance to add the cdr3 seqs you'd add `--extra-annotation-columns cdr3_seqs`. To see other choices, run `./bin/partis annotate --help` (perhaps with `|grep -C3 extra-ann`). This also makes it easy to add anything extra that you want without cluttering up the default output, so if you want something that isn't there just ask.