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Update MartsAdapter #69

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merged 15 commits into from
Sep 9, 2022
Merged

Update MartsAdapter #69

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83e5a78
Rewrite, extend, cleanup MartsAdapter, adapt tests
christopher-mohr Aug 16, 2022
b1df41e
add requests and beautifulsoup4 dependency
christopher-mohr Aug 16, 2022
684f792
prevent too long requests, avoid server request for each attribute
christopher-mohr Aug 16, 2022
26be48e
add gene to test object
christopher-mohr Aug 16, 2022
cdb33d2
fix enum ref
christopher-mohr Aug 16, 2022
e284cb4
adapt MartsAdapter in other test
christopher-mohr Aug 16, 2022
5347113
add function for getting gene names, add tests
christopher-mohr Aug 23, 2022
cf27bc7
change method name, add test
christopher-mohr Aug 23, 2022
c60db7c
add lxml as dependency
christopher-mohr Aug 23, 2022
8ae778f
workaround for pandas read_xml, remove dependency
christopher-mohr Aug 24, 2022
4d85761
add missing all()
christopher-mohr Aug 24, 2022
8c1c870
fix test
christopher-mohr Aug 24, 2022
95c5016
add retry strategy for GET requests
christopher-mohr Aug 25, 2022
04863bb
Update epytope/IO/MartsAdapter.py
christopher-mohr Sep 9, 2022
a25385a
add default biomart url
christopher-mohr Sep 9, 2022
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1 change: 0 additions & 1 deletion epytope/Core/Generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -241,7 +241,6 @@ def _generate_combinations(tId, vs, seq, usedVs, offset, isReverse):

prots = []
for tId, vs in transToVar.items():
#print tId
query = dbadapter.get_transcript_information(tId, type=id_type, _db=db)
if query is None:
logging.warning("Transcript with ID %s not found in DB or sequence unavailable"%tId)
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