Error in calcuating "Radius"

[aoki0623mriid2]

Dear kmayerb,

I run tcrdist3 in docker using the container "quay.io/kmayerb/tcrdist3:0.1.9" For calculating "radius", I tried to load un-enriched repertoire data as documentation, but I faced the following error. I think it is because "unzip" is not installed in the docker container of tcrdist3, but I could not find how to do it.

Best, Hiroyasu

ts = _default_sampler(organism = "mouse", chain = "beta")() ruggiero_mouse_beta_t.tsv.sampler.tsv RUNNING: curl -o /usr/local/lib/python3.8/dist-packages/tcrsampler/db/ruggiero_mouse_sampler.zip https://www.dropbox.com/s/yz8v1c1gf2eyzxk/ruggiero_mouse_sampler.zip?dl=1 -L % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 150 0 150 0 0 622 0 --:--:-- --:--:-- --:--:-- 622 100 320 100 320 0 0 407 0 --:--:-- --:--:-- --:--:-- 0 100 210k 100 210k 0 0 117k 0 0:00:01 0:00:01 --:--:-- 758k sh: 1: unzip: not found

OSError Traceback (most recent call last) /usr/local/lib/python3.8/dist-packages/tcrdist/sample.py in _default_tcrsampler_mouse_beta(default_background, default_background_if_missing) 184 try: --> 185 t = TCRsampler(default_background=default_background) 186 except OSError:

/usr/local/lib/python3.8/dist-packages/tcrsampler/sampler.py in init(self, default_background) 72 if not os.path.isfile(path_to_db_bkgd): ---> 73 raise OSError(f'{path_to_db_bkgd} default file not found. Download a default background using python -c "from tcrsampler.setup_db import install_all_next_gen; install_all_next_gen(dry_run = False)"') 74 else:

OSError: /usr/local/lib/python3.8/dist-packages/tcrsampler/db/ruggiero_mouse_beta_t.tsv.sampler.tsv default file not found. Download a default background using python -c "from tcrsampler.setup_db import install_all_next_gen; install_all_next_gen(dry_run = False)"

During handling of the above exception, another exception occurred:

OSError Traceback (most recent call last)

in ----> 1 ts = _default_sampler(organism = "mouse", chain = "beta")() /usr/local/lib/python3.8/dist-packages/tcrdist/sample.py in _default_tcrsampler_mouse_beta(default_background, default_background_if_missing) 187 t = TCRsampler() 188 t.download_background_file(default_background_if_missing) --> 189 t = TCRsampler(default_background=default_background) 190 return t 191 /usr/local/lib/python3.8/dist-packages/tcrsampler/sampler.py in __init__(self, default_background) 71 path_to_db_bkgd = os.path.join(path_to_db, self.default_bkgd) 72 if not os.path.isfile(path_to_db_bkgd): ---> 73 raise OSError(f'{path_to_db_bkgd} default file not found. Download a default background using python -c "from tcrsampler.setup_db import install_all_next_gen; install_all_next_gen(dry_run = False)"') 74 else: 75 bar = IncrementalBar(f'Loading {self.default_bkgd}', max = 2, suffix='%(percent)d%%') OSError: /usr/local/lib/python3.8/dist-packages/tcrsampler/db/ruggiero_mouse_beta_t.tsv.sampler.tsv default file not found. Download a default background using python -c "from tcrsampler.setup_db import install_all_next_gen; install_all_next_gen(dry_run = False)"

[kmayerb]

Thanks for alerting us of this issue, I think it would be a good idea to add unzip to the docker image. I am adding that so it will be pre-installed in tcrdist:0.2.3

For now a quick fix would be the following:

docker run -it quay.io/kmayerb/tcrdist3:0.2.2

Then within the container:

apt-get install unzip

Then this works just fine:

from tcrdist.sample import _default_sampler
ts = _default_sampler(organism = "mouse", chain = "beta")()

[aoki0623mriid2]

Thank you for your kined reply.

I found the code run successfully with your instruction. Thank you so much for your kindness.

[kmayerb]

No problem at all. Thank you for bringing this issue to our attention.