pheval 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

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Files changed (12) hide show
  1. pheval/analyse/benchmark_db_manager.py +2 -2
  2. pheval/analyse/disease_prioritisation_analysis.py +2 -2
  3. pheval/analyse/gene_prioritisation_analysis.py +2 -2
  4. pheval/analyse/parse_corpus.py +7 -7
  5. pheval/analyse/rank_stats.py +3 -3
  6. pheval/analyse/variant_prioritisation_analysis.py +2 -2
  7. pheval/prepare/prepare_corpus.py +6 -2
  8. {pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/METADATA +1 -1
  9. {pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/RECORD +12 -12
  10. {pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/WHEEL +1 -1
  11. {pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/LICENSE +0 -0
  12. {pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/entry_points.txt +0 -0
pheval/analyse/benchmark_db_manager.py CHANGED
@@ -47,9 +47,9 @@ class BenchmarkDBManager:
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  """
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  try:
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  self.conn.execute(
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- f'ALTER TABLE {table_name} ADD COLUMN "{column}" INTEGER DEFAULT {default}'
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+ f'ALTER TABLE "{table_name}" ADD COLUMN "{column}" INTEGER DEFAULT {default}'
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  )
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- self.conn.execute(f'UPDATE {table_name} SET "{column}" = ?', (default,))
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+ self.conn.execute(f'UPDATE "{table_name}" SET "{column}" = ?', (default,))
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  self.conn.commit()
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  except duckdb.CatalogException:
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  pass
pheval/analyse/disease_prioritisation_analysis.py CHANGED
@@ -32,7 +32,7 @@ class AssessDiseasePrioritisation(AssessPrioritisationBase):
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  """
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  relevant_ranks = []
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  df = self.conn.execute(
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- f"SELECT * FROM {self.table_name} WHERE phenopacket = ? ",
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+ f"SELECT * FROM '{self.table_name}' WHERE phenopacket = ? ",
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  (phenopacket_path.name,),
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  ).fetchdf()
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  for _i, row in df.iterrows():
@@ -58,7 +58,7 @@ class AssessDiseasePrioritisation(AssessPrioritisationBase):
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  relevant_ranks.append(disease_match)
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  primary_key = f"{phenopacket_path.name}-{row['disease_identifier']}"
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  self.conn.execute(
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- f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
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+ f'UPDATE "{self.table_name}" SET "{self.column}" = ? WHERE identifier = ?',
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  (disease_match, primary_key),
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  )
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  elif len(result) == 0:
pheval/analyse/gene_prioritisation_analysis.py CHANGED
@@ -31,7 +31,7 @@ class AssessGenePrioritisation(AssessPrioritisationBase):
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  """
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  relevant_ranks = []
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  df = self.conn.execute(
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- f"""SELECT * FROM {self.table_name} WHERE phenopacket = '{phenopacket_path.name}'"""
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+ f"""SELECT * FROM "{self.table_name}" WHERE phenopacket = '{phenopacket_path.name}'"""
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  ).fetchdf()
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  for _i, row in df.iterrows():
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  result = (
@@ -55,7 +55,7 @@ class AssessGenePrioritisation(AssessPrioritisationBase):
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  relevant_ranks.append(gene_match)
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  primary_key = f"{phenopacket_path.name}-{row['gene_symbol']}"
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  self.conn.execute(
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- f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
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+ f'UPDATE "{self.table_name}" SET "{self.column}" = ? WHERE identifier = ?',
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  (gene_match, primary_key),
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  )
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  if not result:
pheval/analyse/parse_corpus.py CHANGED
@@ -81,7 +81,7 @@ class CorpusParser:
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  """
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  self.conn.execute(
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  f"""
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- CREATE TABLE IF NOT EXISTS {self.table_name}_gene (
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+ CREATE TABLE IF NOT EXISTS "{self.table_name}_gene" (
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  identifier VARCHAR(255) PRIMARY KEY,
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  phenopacket VARCHAR,
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  gene_symbol VARCHAR,
@@ -96,7 +96,7 @@ class CorpusParser:
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  """
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  self.conn.execute(
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  f"""
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- CREATE TABLE IF NOT EXISTS {self.table_name}_variant (
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+ CREATE TABLE IF NOT EXISTS "{self.table_name}_variant" (
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  identifier VARCHAR(255) PRIMARY KEY,
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  phenopacket VARCHAR,
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  chrom VARCHAR,
@@ -113,7 +113,7 @@ class CorpusParser:
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  """
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  self.conn.execute(
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  f"""
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- CREATE TABLE IF NOT EXISTS {self.table_name}_disease (
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+ CREATE TABLE IF NOT EXISTS "{self.table_name}_disease" (
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  identifier VARCHAR(255) PRIMARY KEY,
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  phenopacket VARCHAR,
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  disease_identifier VARCHAR,
@@ -147,7 +147,7 @@ class CorpusParser:
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  identifier = f"{phenopacket_path.name}-{gene.gene_symbol}"
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  self.conn.execute(
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  f"""
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- INSERT OR IGNORE INTO {self.table_name}_gene (identifier, phenopacket, gene_symbol, gene_identifier)
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+ INSERT OR IGNORE INTO "{self.table_name}_gene" (identifier, phenopacket, gene_symbol, gene_identifier)
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  VALUES (?, ?, ?, ?)
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  """,
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  (identifier, phenopacket_path.name, gene.gene_symbol, gene.gene_identifier),
@@ -166,7 +166,7 @@ class CorpusParser:
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  )
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  self.conn.execute(
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  f"""
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- INSERT OR IGNORE INTO {self.table_name}_variant (identifier, phenopacket, chrom, pos, "ref", alt)
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+ INSERT OR IGNORE INTO "{self.table_name}_variant" (identifier, phenopacket, chrom, pos, "ref", alt)
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  VALUES (?, ?, ?, ?, ?, ?)
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  """,
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  (
@@ -189,8 +189,8 @@ class CorpusParser:
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  for disease in diseases:
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  identifier = f"{phenopacket_path.name}-{disease.disease_identifier}"
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  self.conn.execute(
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- f"INSERT OR IGNORE INTO {self.table_name}_disease "
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- f"(identifier, phenopacket, disease_identifier, disease_name) VALUES (?, ?, ?, ?)",
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+ f"""INSERT OR IGNORE INTO "{self.table_name}_disease" """
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+ f"""(identifier, phenopacket, disease_identifier, disease_name) VALUES (?, ?, ?, ?)""",
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  (
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  identifier,
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  phenopacket_path.name,
pheval/analyse/rank_stats.py CHANGED
@@ -68,7 +68,7 @@ class RankStats:
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  Returns:
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  int: Count query result.
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  """
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- query = f'SELECT COUNT(*) FROM {table_name} WHERE "{column_name}" {condition}'
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+ query = f'SELECT COUNT(*) FROM "{table_name}" WHERE "{column_name}" {condition}'
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  return conn.execute(query).fetchone()[0]
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  @staticmethod
@@ -85,7 +85,7 @@ class RankStats:
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  Returns:
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  List[float]: List of reciprocal ranks.
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  """
88
- query = f'SELECT "{column_name}" FROM {table_name}'
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+ query = f'SELECT "{column_name}" FROM "{table_name}"'
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  return [1 / rank[0] if rank[0] > 0 else 0 for rank in conn.execute(query).fetchall()]
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  @staticmethod
@@ -103,7 +103,7 @@ class RankStats:
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  List[List[int]]: List of relevant ranks.
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  """
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  query = (
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- f'SELECT LIST("{column_name}") as values_list FROM {table_name} GROUP BY phenopacket'
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+ f'SELECT LIST("{column_name}") as values_list FROM "{table_name}" GROUP BY phenopacket'
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  )
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  return [rank[0] for rank in conn.execute(query).fetchall()]
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pheval/analyse/variant_prioritisation_analysis.py CHANGED
@@ -33,7 +33,7 @@ class AssessVariantPrioritisation(AssessPrioritisationBase):
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  """
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  relevant_ranks = []
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  df = self.conn.execute(
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- f"""SELECT * FROM {self.table_name} WHERE phenopacket = '{phenopacket_path.name}'"""
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+ f"""SELECT * FROM "{self.table_name}" WHERE phenopacket = '{phenopacket_path.name}'"""
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  ).fetchdf()
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  for _i, row in df.iterrows():
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  causative_variant = GenomicVariant(
@@ -67,7 +67,7 @@ class AssessVariantPrioritisation(AssessPrioritisationBase):
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  f"{causative_variant.ref}-{causative_variant.alt}"
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  )
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  self.conn.execute(
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- f'UPDATE {self.table_name} SET "{self.column}" = ? WHERE identifier = ?',
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+ f'UPDATE "{self.table_name}" SET "{self.column}" = ? WHERE identifier = ?',
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  (variant_match, primary_key),
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  )
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  elif len(result) == 0:
pheval/prepare/prepare_corpus.py CHANGED
@@ -90,6 +90,10 @@ def prepare_corpus(
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  )
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  else:
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  # if not updating phenopacket gene identifiers then copy phenopacket as is to output directory
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- shutil.copy(
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- phenopacket_path, output_dir.joinpath(f"phenopackets/{phenopacket_path.name}")
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+ (
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+ shutil.copy(
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+ phenopacket_path, output_dir.joinpath(f"phenopackets/{phenopacket_path.name}")
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+ )
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+ if phenopacket_path != output_dir.joinpath(f"phenopackets/{phenopacket_path.name}")
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+ else None
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  )
{pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
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  Name: pheval
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- Version: 0.4.3
3
+ Version: 0.4.5
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  Summary:
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  Author: Yasemin Bridges
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  Author-email: y.bridges@qmul.ac.uk
{pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/RECORD RENAMED
@@ -2,20 +2,20 @@ pheval/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
2
  pheval/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
3
3
  pheval/analyse/analysis.py,sha256=Yt2xH0WS_2NO13-wYvywzmCRCj8RinQ1MeozJQuGe3o,4009
4
4
  pheval/analyse/assess_prioritisation_base.py,sha256=znBscRTqIKxxZMHR-H6KrjFJ6Uv5P5HzwTQUWS6Eoos,3434
5
- pheval/analyse/benchmark_db_manager.py,sha256=R1GstKKoh4PIPupyAarm7DhZyOdVDVtyY4A1nPNTkDs,5181
5
+ pheval/analyse/benchmark_db_manager.py,sha256=IRqu5fUpLBboHpS4lx0AaAkor_W7whuvUSKiMr2-GhM,5185
6
6
  pheval/analyse/benchmark_generator.py,sha256=-LljszuKAT3oJfGQn7JHAILCGg5QXYny4nPPf273g_E,5896
7
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  pheval/analyse/benchmarking_data.py,sha256=aRvDmwqjFGKvWDRGjMwaQxfDZscptRBwI-rcSqY-X5s,913
8
8
  pheval/analyse/binary_classification_stats.py,sha256=E35YjvGM-zFnuEt8M3pgN03vBab4MH6ih726QKvuogg,12519
9
- pheval/analyse/disease_prioritisation_analysis.py,sha256=mOIAiz_WzWQBP-3g8Twv-ii8ZxbXktAmgi6zl4sJaC8,6182
10
- pheval/analyse/gene_prioritisation_analysis.py,sha256=wPH-mCW_KY3XxrwAvw-ucxLbWzUKBucO4zSo3XqBsaY,6022
9
+ pheval/analyse/disease_prioritisation_analysis.py,sha256=t__1lhyw1PnbDBbXDxDaFgLFbdRz20D1s-8tfLQJjLs,6186
10
+ pheval/analyse/gene_prioritisation_analysis.py,sha256=Bapg0VcHOz5vp1dI4bDba04SpX6UdDu35VGTI6sZyOk,6026
11
11
  pheval/analyse/generate_plots.py,sha256=5oxsdnAbbVgQj8ZrWTLs12rSM24EXp-IdLCjy5QB1_g,21992
12
12
  pheval/analyse/generate_summary_outputs.py,sha256=nKqwbpA-9bbL5mCySiuyV_AUDIokmCg3vD8_JAsg1ls,4157
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  pheval/analyse/parse_benchmark_summary.py,sha256=vyAOIdIWF4rZjGTPFE69ajhEC9AkkN3QBVqSe_uYZsg,2946
14
- pheval/analyse/parse_corpus.py,sha256=N88enptR4qG6cmqXU_TKg8DMmCeFog37eeK5nFEMQOQ,8678
14
+ pheval/analyse/parse_corpus.py,sha256=pxhoKTgd-DnwAMP081UMG-NKbj89qAYBQhHve8aphfI,8698
15
15
  pheval/analyse/prioritisation_result_types.py,sha256=qJoB6O-lFYmzAMcTQeDJZQNLJ6hleoKDYATTkhvFF98,1228
16
- pheval/analyse/rank_stats.py,sha256=53ZickUtQlctYsorAIUwlCX7M6UC-wCxoV1MbL6F9gc,17987
16
+ pheval/analyse/rank_stats.py,sha256=vNLVuG_NzhKDXxKmklYNPz44MczlyKUqcuHqbiuOXwI,17993
17
17
  pheval/analyse/run_data_parser.py,sha256=VQBUoOIRYRWc5uqURUvaWdaW3E3C7Su0JvLavQLHQaY,4105
18
- pheval/analyse/variant_prioritisation_analysis.py,sha256=8ntbALzAAfJ4ijviQKvLiwKBeRvTLWI0Tb9dpnCYxhs,6404
18
+ pheval/analyse/variant_prioritisation_analysis.py,sha256=HhDeczF7wmJjXt0ejAtF0qdczyMe25glqiS6uX_TFl8,6408
19
19
  pheval/cli.py,sha256=EBGh6TIxAiWs0eDdQiefq6YuD0mb93siGsNmsVO1j7c,1527
20
20
  pheval/cli_pheval.py,sha256=fWbKUcPTZZSa1EJEtH_lNn1XE6qRApRHihqUZS5owrA,2424
21
21
  pheval/cli_pheval_utils.py,sha256=O6tWnE85QQHGNcP08OwJGANMfXJPsZtFEu-D6ATld00,16700
@@ -29,7 +29,7 @@ pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
29
29
  pheval/prepare/create_noisy_phenopackets.py,sha256=ydhA4mpqKTDc4hBu8YfvNW2nMubHK3dbO-cv0lA4JFQ,11504
30
30
  pheval/prepare/create_spiked_vcf.py,sha256=90A-Mi8QKhvN036vtFEVWAHgzHO37itiLYrqYlG4LiA,23953
31
31
  pheval/prepare/custom_exceptions.py,sha256=_G3_95dPtHIs1SviYBV1j7cYc-hxlhuw8hhnYdzByYY,1719
32
- pheval/prepare/prepare_corpus.py,sha256=mwI3FJJ6GGSbmbvz4enrVP86MBoHSssMIRebkapmu5Y,4484
32
+ pheval/prepare/prepare_corpus.py,sha256=YFnklpeVXeqeme9DVmd_jfsK04ytIe9cH5uXYcgK5cY,4650
33
33
  pheval/prepare/update_phenopacket.py,sha256=21fzUPbwKN6Ey5TSh9PFzjT2x86U19RAE6WmkjG8u28,4770
34
34
  pheval/resources/alternate_ouputs/CADA_results.txt,sha256=Rinn2TtfwFNsx0aEWegKJOkjKnBm-Mf54gdaT3bWP0k,547
35
35
  pheval/resources/alternate_ouputs/DeepPVP_results.txt,sha256=MF9MZJYa4r4PEvFzALpi-lNGLxjENOnq_YgrgFMn-oQ,1508
@@ -50,8 +50,8 @@ pheval/utils/file_utils.py,sha256=m21cz-qjDYqnI8ClUv3J9fKizex98a-9bSEerQ75i_c,35
50
50
  pheval/utils/phenopacket_utils.py,sha256=6xQ8WCLdR1VhiU3nCDzaqEVKjGvDWrzvPA50_6ZAHXM,27310
51
51
  pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
52
52
  pheval/utils/utils.py,sha256=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
53
- pheval-0.4.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
54
- pheval-0.4.3.dist-info/METADATA,sha256=Y6dy74TNnyirSwcpgG9ktJopwoVEZWlixSR4CJOZfDo,6469
55
- pheval-0.4.3.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
56
- pheval-0.4.3.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
57
- pheval-0.4.3.dist-info/RECORD,,
53
+ pheval-0.4.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
54
+ pheval-0.4.5.dist-info/METADATA,sha256=fUGgR-undfldkiVtLHXx1AjoN4gaweABMbbk79Qp0cA,6469
55
+ pheval-0.4.5.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
56
+ pheval-0.4.5.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
57
+ pheval-0.4.5.dist-info/RECORD,,
{pheval-0.4.3.dist-info → pheval-0.4.5.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
1
1
  Wheel-Version: 1.0
2
- Generator: poetry-core 2.0.0
2
+ Generator: poetry-core 2.0.1
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any