pinellolab / primedesign Goto Github PK

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

License: Other

Dockerfile 0.39% Shell 0.04% Python 95.90% CSS 3.67%

primedesign's Issues

Inserts longer than 33 bp are not supported?

Hi! I am trying to generate a pegRNA to use for twin prime editing, i.e. inserting the full AttB site at a genomic site of interest, as discussed in this paper. Yet, AttB site is at least 38 bp long, while any insertion longer than 33 bp yields N/A as a suggested pegRNA. Is there an easy fix that doesn't involve re-training the model with longer inserts?

Nicking Dist Min and max no longer function

python /seqprg/scripts/gene_editing/primedesign.py -f design.txt -pbs 10 11 12 13 14 15 -rtt 10 11 12 -nick_dist_max 10

2022-07-28 21:00:47,188 - INFO - Searching for pegRNAs and nicking gRNAs for target sequences ...
Traceback (most recent call last):
File "/seqprg/scripts/gene_editing/primedesign.py", line 1359, in
if (abs(nick_distance) >= nicking_distance_minimum) and (abs(nick_distance) <= nicking_distance_maximum):
TypeError: '<=' not supported between instances of 'int' and 'list'

If I do not use the nicking distance min and max, then the tools functions fine. But when I go to pass in a number, I keep getting this error. This just started recently

SCN5A site in Supplementary Data 2 not correct?

Hello,

Please see the illustration. The expected mutation from PrimeDesign Input is G4CTTCT. When mapping the PBS and RTT sequences, the mutation I got is actually the deletion of CTGGGGCTT.

Thanks,
Yichao

Failure to generate guides when CFD scores are to be calculated on locally (and publicly?) hosted client.

Hello,

I am once again trying to calculate CFD scores for a set of guides, but if I have "Calculate CFD score" switched to "Yes", then there is no output. This seems to be true for the publicly hosted client, and it is certainly true for the locally hosted client. Here is my terminal output as I first change my desired settings in "Prime editing parameters" and then paste in the correctly formated sequence and edit:

[2021-02-27 00:39:27 +0000] [8] [INFO] Starting gunicorn 20.0.4
[2021-02-27 00:39:27 +0000] [8] [INFO] Listening at: http://0.0.0.0:9994 (8)
[2021-02-27 00:39:27 +0000] [8] [INFO] Using worker: sync
[2021-02-27 00:39:27 +0000] [10] [INFO] Booting worker with pid: 10
[2021-02-27 00:39:27 +0000] [11] [INFO] Booting worker with pid: 11
[2021-02-27 00:39:27 +0000] [12] [INFO] Booting worker with pid: 12
[2021-02-27 00:39:27 +0000] [13] [INFO] Booting worker with pid: 13
172.17.0.1 - - [27/Feb/2021:00:39:32 +0000] "GET / HTTP/1.1" 200 618 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "GET /_dash-dependencies HTTP/1.1" 200 1205 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "GET /_dash-layout HTTP/1.1" 200 568 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 3528 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 42 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 3528 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:33 +0000] "POST /_dash-update-component HTTP/1.1" 200 40 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 146 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 147 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 263 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 69 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 75 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 263 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:34 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:35 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:42 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:45 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:46 +0000] "POST /_dash-update-component HTTP/1.1" 200 63 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:47 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:49 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:49 +0000] "POST /_dash-update-component HTTP/1.1" 200 349 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:50 +0000] "POST /_dash-update-component HTTP/1.1" 200 37 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
ERROR! /PrimeDesign/hg38_chromosomes is not a directory.
Exception on /_dash-update-component [POST]
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/opt/conda/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1461, in dispatch
    response.set_data(self.callback_map[output]["callback"](*args))
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1341, in add_context
    output_value = func(*args, **kwargs)  # %% callback invoked %%
  File "/PrimeDesign/web_app/app.py", line 3607, in run_primedesign
    with open('/PrimeDesign/web_app/crispritz_output_%s.scores.txt' % session_id, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/PrimeDesign/web_app/crispritz_output_20210227_12.39.33.61.scores.txt'
172.17.0.1 - - [27/Feb/2021:00:39:52 +0000] "POST /_dash-update-component HTTP/1.1" 500 290 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:58 +0000] "POST /_dash-update-component HTTP/1.1" 200 139 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 200 83 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 200 359 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"
ERROR! /PrimeDesign/hg38_chromosomes is not a directory.
Exception on /_dash-update-component [POST]
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/opt/conda/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/conda/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1461, in dispatch
    response.set_data(self.callback_map[output]["callback"](*args))
  File "/opt/conda/lib/python3.8/site-packages/dash/dash.py", line 1341, in add_context
    output_value = func(*args, **kwargs)  # %% callback invoked %%
  File "/PrimeDesign/web_app/app.py", line 3607, in run_primedesign
    with open('/PrimeDesign/web_app/crispritz_output_%s.scores.txt' % session_id, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/PrimeDesign/web_app/crispritz_output_20210227_12.39.33.61.scores.txt'
172.17.0.1 - - [27/Feb/2021:00:39:59 +0000] "POST /_dash-update-component HTTP/1.1" 500 290 "http://localhost:9994/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36"

Thank you!

CFD Scores aren't in "Download Designs" spreadsheet

I have been using the hosted PrimeDesign at https://drugthatgene.pinellolab.partners.org/. I have checked the option to calcuate CFD score, and these scores do display correctly in my browser for the sgRNAs. However, when I download designs using the "Download Designs" button, there is a column for CFD score in the spreadsheet for which no values are given. I suspect this is a bug.

Flag duplicate ngRNA oligos when designing multiple guides

When designing multiple pegRNAs + ngRNAs for a given gene using the PE3 or PE3b strategy , the set of ngRNAs identified for each pegRNA may end up being the same sequence. To avoid manual quality control of sequences, duplication of purchases of oligos, and duplication of cloning, it would be useful to flag the ngRNA sequences output as duplicates or identical sequences at alert the user. Either adding another column to the output csv or a warning on the web tool / Docker output.

Web interface returning '502 Bad Gateway'

Hi,

I have noticed the web interface @ https://primedesign.pinellolab.partners.org/ is directing to a '502 Bad Gateway' page.

Thanks,
Dan

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