Mercurial > repos > tduigou > seq_to_db

annotate verification.py @ 0:178d068648f4 draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
author tduigou
date Thu, 12 Jun 2025 08:27:18 +0000
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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1 from sqlalchemy import create_engine, text
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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3 db_uri = "postgresql://postgres:RK17@localhost:5432/test_fragments_db" # adapt with your URI's DB
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
4 engine = create_engine(db_uri)
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
6 with engine.connect() as conn:
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
7 result = conn.execute(text("""
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
8 SELECT fragment, sequence, annotation
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
9 FROM sample
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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10 ORDER BY fragment
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
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11 """))
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
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12
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
13 print("Full contents of fragments in DB:\n")
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
14 for row in result:
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
15 print(f" Fragment: {row.fragment}")
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
16 print(" Sequence:")
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
17 print(row.sequence)
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
18 print("\n Annotation:")
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
19 print(row.annotation)
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
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20 print("-" * 80)