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althonos / pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
https://pyopal.readthedocs.io
MIT License
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Wrong error message #2

Closed valentynbez closed 1 year ago

valentynbez commented 1 year ago 
import pyopal

database = pyopal.Database([
    "MESILDLQELETSEEESALMAASTVSNNC",                         # goadvionin A
    "MKKAVIVENKGCATCSIGAACLVDGPIPDFEIAGATGLFGLWG",           # subtilosin A
    "MAGFLKVVQILAKYGSKAVQWAWANKGKILDWINAGQAIDWVVEKIKQILGIK", # lacticin Z
    "MTQIKVPTALIASVHGEGQHLFEPMAARCTCTTIISSSSTF",             # plantazolicin
])

queries = ["MAGFLKVVQLLAKYGSKAVQWAWANKGKILDWLNAGQAIDWVVSKIKQILGIK"] * 4
results = database.search(queries[0], algorithm="nw", mode="full", overflow="bucket")
File pyopal/_opal.pyx:1041, in pyopal._opal.Database.search()

ValueError: Invalid overflow mode: 'full'
althonos commented 1 year ago

Fixed in v0.3.0.