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36 lines
872 B
Python
36 lines
872 B
Python
import os
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import shutil
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import subprocess as sp
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from Bio import SeqIO
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from dscript.language_model import (
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lm_embed,
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embed_from_fasta,
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)
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class TestLanguageModel:
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@classmethod
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def setup_class(cls):
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cmd = "python setup.py install"
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proc = sp.Popen(cmd.split())
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proc.wait()
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os.makedirs("./tmp-dscript-testing/", exist_ok=True)
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@classmethod
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def teardown_class(cls):
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shutil.rmtree("./tmp-dscript-testing/")
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def test_lm_embed(self):
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seqs = list(SeqIO.parse("dscript/tests/test.fasta", "fasta"))
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for seqrec in seqs:
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x = lm_embed(str(seqrec.seq))
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assert x.shape[1] == len(seqrec.seq)
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def embed_from_fasta(self):
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embed_from_fasta(
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"dscript/tests/test.fasta",
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"tmp-dscript-testing/test_embed.h5",
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verbose=True,
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)
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