Comments (4)
from pheweb.
This is what I see in the STDOUT:
sudo pheweb serve --port 33098
[2023-09-17 20:13:55 +0900] [32421] [INFO] Starting gunicorn 20.0.4
[2023-09-17 20:13:55 +0900] [32421] [INFO] Listening at: http://0.0.0.0:33098 (32421)
[2023-09-17 20:13:55 +0900] [32421] [INFO] Using worker: gevent
[2023-09-17 20:13:55 +0900] [32425] [INFO] Booting worker with pid: 32425
[2023-09-17 20:13:55 +0900] [32426] [INFO] Booting worker with pid: 32426
[2023-09-17 20:13:55 +0900] [32427] [INFO] Booting worker with pid: 32427
[2023-09-17 20:13:55 +0900] [32428] [INFO] Booting worker with pid: 32428
[2023-09-17 20:13:55 +0900] [32429] [INFO] Booting worker with pid: 32429
[2023-09-17 20:13:55 +0900] [32430] [INFO] Booting worker with pid: 32430
[2023-09-17 20:13:55 +0900] [32431] [INFO] Booting worker with pid: 32431
[2023-09-17 20:13:55 +0900] [32432] [INFO] Booting worker with pid: 32432
When I click a variant name:
Exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/pheweb/serve/server.py", line 120, in variant_page
variant = get_variant(query)
File "/usr/local/lib/python3.6/dist-packages/pheweb/serve/server_utils.py", line 70, in get_variant
assert None not in [chrom, pos, ref, alt]
AssertionError
Oh no, something went wrong
[17/Sep/2023:20:45:50 +0900] | 404 | 0.020327s | GET /variant/4-10211261-C-<DEL> | resp_len:3825 | referrer:"http://210.114.91.250:33098/phenotypes" | ip:183.100.201.22 | agent:Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.0.0 Safari/537.36
[17/Sep/2023:20:45:50 +0900] | 200 | 0.002083s | GET /static/common.css | resp_len:397 | referrer:"http://210.114.91.250:33098/variant/4-10211261-C-%3CDEL%3E" | ip:183.100.201.22 | agent:Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.0.0 Safari/537.36
[17/Sep/2023:20:45:50 +0900] | 200 | 0.001662s | GET /static/common.js | resp_len:1092 | referrer:"http://210.114.91.250:33098/variant/4-10211261-C-%3CDEL%3E" | ip:183.100.201.22 | agent:Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.0.0 Safari/537.36
from pheweb.
Hi,
I modified one line in class "_ParseVariant" and now I can see the phewas plot.
#chrom_pos_ref_alt_regex = re.compile(chrom_pos_regex.pattern + r'[-_:/ ]([-AaTtCcGg\.]+)[-_:/ ]([-AaTtCcGg\.]+)')
chrom_pos_ref_alt_regex = re.compile(chrom_pos_regex.pattern + r'[-_:/ ]([-AaTtCcGg\.]+)[-_:/ ]([A-Za-z\-<>\.]+)')
My URL was /variant/4-10211261-C-<DEL>
, so I changed the code to allow any alphabet and <> as the alternate allele.
Thank you.
from pheweb.
from pheweb.
Related Issues (20)
- Core features of pheweb: ref/alt, add_rsid, hg17/38 HOT 3
- stroke
- ModuleNotFoundError: No module named 'pheweb.command_line' HOT 3
- "An exception occurred" when I run the command: pheweb serve --open HOT 3
- pheweb to display multiple GWAS? HOT 1
- outdated instruction "pheweb phenolist glob-files" HOT 2
- PheWeb can display phenotype correlations generated by another tool. HOT 4
- pheweb-rg-pipeline does NOT work HOT 1
- Installation Problem HOT 7
- METSIM Pheweb Instance Not Working HOT 1
- the content of pheweb HOT 1
- Not clear when 3 parts of pheweb (executable, python scripts, huge dbSNP files) got installed HOT 1
- how to display the phenotypes in sorted order? HOT 9
- Starting `pheweb add-rsids`, Completed in 57 minutes HOT 2
- interpretation HOT 1
- after i renamed the input GWAS files HOT 5
- pheweb.utils.PheWebError: failed on field 'af' attempting to convert value 'NA' to type <class 'float'>
- Some Manhattan Plots don't show up HOT 5
- `pheweb augment-phenos` takes hours for just one single new GWAS HOT 2
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from pheweb.