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InsecureRequestWarning for Pfam functionality #14

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locitran opened this issue Dec 1, 2023 · 0 comments
Open

InsecureRequestWarning for Pfam functionality #14

locitran opened this issue Dec 1, 2023 · 0 comments

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@locitran
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locitran commented Dec 1, 2023

Dear Rhapsody developers,

I have encountered InsecureRequestWarning for Pfam request. It seems pfam-legacy.xfam.org is unverified so that the Pfam-related features cannot be calculated. Do anyone get this problem as mine? Thank you.

import rhapsody as rd
SAVs = ['O00206 188 Q R']
f = rd.Pfam.calcPfamFeatures(SAVs)

@> Retrieving Pfam search results: https://pfam-legacy.xfam.org/protein/O00206?output=xml
/opt/miniconda3/envs/project/lib/python3.9/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'pfam-legacy.xfam.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
@> Pfam search completed in 2.19s.
@> WARNING Unable to compute Pfam features: failed to parse results XML, check URL: https://pfam-legacy.xfam.org/protein/O00206?output=xml
@> Pickle 'UniprotMap-O00206.pkl' saved.
Mapping SAV 'O00206 188 Q R' to Pfam: 100%|??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????| 1/1 [00:48<00:00]
@> SAVs have been mapped on Pfam domains and sequence properties have been computed in 48.6s.

Besides this function, EVmutation is not working for my case. Looking forward to hearing the feedback. Thank you

f = rd.EVmutation.recoverEVmutFeatures(SAVs)
@> Recovering EVmutation data...
@> EVmutation scores recovered in 0.2s.
>>> f
array([(nan, nan)], dtype=[('entropy', '<f4'), ('ranked_MI', '<f4')])

Loci.

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