PyEvoMotion 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

share/generate_sequences_from_synthdata.py

@@ -0,0 +1,85 @@
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                           IMPORTS                          #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+import numpy as np
+import pandas as pd
+
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                          CONSTANTS                         #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+WUHAN_REF_PATH = "tests/data/test3/test3UK.fasta"
+DATE_MAP = dict(zip(
+    range(41),
+    pd.date_range(start="2020-01-01", periods=41, freq="7D")
+))
+NUCLEOTIDES = {"A", "C", "G", "T"}
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                          FUNCTIONS                         #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+def load_synthdata(path: str) -> pd.DataFrame:
+    """Loads the synthdata from the given path.
+    """
+
+    df = pd.read_csv(path, sep="\t", index_col=0)
+    df.columns = [f"seq{k}" for k in range(len(df.columns))]
+
+    return df
+
+def get_wuhan_ref() -> SeqRecord:
+    """Returns the Wuhan reference sequence.
+    """
+    # We know the Wuhan sequence is the first one in the file
+    with open(WUHAN_REF_PATH, "r") as f:
+        for record in SeqIO.parse(f, "fasta"):
+            return record
+
+def create_synthetic_sequence(mut_num: int, wuhan_ref: SeqRecord) -> str:
+    """Creates a synthetic sequence from the Wuhan reference sequence.
+    """
+    _seq = list(wuhan_ref.seq)
+    mut_positions = np.random.choice(range(len(_seq)), mut_num, replace=False)
+    nucleotides = [
+        np.random.choice(list(NUCLEOTIDES - {_seq[i]}))
+        for i in mut_positions
+    ]
+    for pos, nuc in zip(mut_positions, nucleotides):
+        _seq[pos] = nuc
+    return "".join(_seq)
+
+
+def create_synthetic_sequences(output_path: str, synthdata: pd.DataFrame, wuhan_ref: SeqRecord) -> None:
+    """Creates the synthetic dataset from the synthdata reference and the Wuhan reference sequence.
+    """
+    with open(f"{output_path}.fasta", "w") as f, open(f"{output_path}.tsv", "w") as g:
+        f.write(f">{wuhan_ref.id}\n{wuhan_ref.seq}\n")
+        g.write(f"id\tdate\n{wuhan_ref.id}\t2019-12-29\n")
+        for row_idx, row in synthdata.iterrows():
+            for col_name, col in row.items():
+                # Fetch the row number, the column name and the entry in the synthdata
+                f.write(f">{col_name}_{row_idx}\n{create_synthetic_sequence(col, wuhan_ref)}\n")
+                g.write(f"{col_name}_{row_idx}\t{DATE_MAP[row_idx].strftime('%Y-%m-%d')}\n")
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                           MAIN                             #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+def main():
+    WUHAN_REF = get_wuhan_ref()
+
+    for name in ("synthdata1", "synthdata2"):
+        create_synthetic_sequences(
+            f"{name}",
+            load_synthdata(f"tests/data/test4/{name}.txt"),
+            WUHAN_REF
+        )
+    print("Synthetic datasets created successfully.")
+
+if __name__ == "__main__":
+    main()

share/generate_sequences_from_test5_data.py

@@ -0,0 +1,107 @@
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                           IMPORTS                          #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+import os
+import numpy as np
+import pandas as pd
+
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                          CONSTANTS                         #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+WUHAN_REF_PATH = "tests/data/test3/test3UK.fasta"
+DATE_MAP = dict(zip(
+    range(41),
+    pd.date_range(start="2020-01-01", periods=41, freq="7D")
+))
+NUCLEOTIDES = {"A", "C", "G", "T"}
+TEST5_BASE_PATH = "tests/data/test5"
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                          FUNCTIONS                         #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+def load_synthdata(path: str) -> pd.DataFrame:
+    """Loads the synthdata from the given path.
+    """
+
+    df = pd.read_csv(path, sep="\t", index_col=0)
+    df.columns = [f"seq{k}" for k in range(len(df.columns))]
+
+    return df
+
+def get_wuhan_ref() -> SeqRecord:
+    """Returns the Wuhan reference sequence.
+    """
+    # We know the Wuhan sequence is the first one in the file
+    with open(WUHAN_REF_PATH, "r") as f:
+        for record in SeqIO.parse(f, "fasta"):
+            return record
+
+def create_synthetic_sequence(mut_num: int, wuhan_ref: SeqRecord) -> str:
+    """Creates a synthetic sequence from the Wuhan reference sequence.
+    """
+    _seq = list(wuhan_ref.seq)
+    mut_positions = np.random.choice(range(len(_seq)), mut_num, replace=False)
+    nucleotides = [
+        np.random.choice(list(NUCLEOTIDES - {_seq[i]}))
+        for i in mut_positions
+    ]
+    for pos, nuc in zip(mut_positions, nucleotides):
+        _seq[pos] = nuc
+    return "".join(_seq)
+
+
+def create_synthetic_sequences(output_path: str, synthdata: pd.DataFrame, wuhan_ref: SeqRecord) -> None:
+    """Creates the synthetic dataset from the synthdata reference and the Wuhan reference sequence.
+    """
+    with open(f"{output_path}.fasta", "w") as f, open(f"{output_path}.tsv", "w") as g:
+        f.write(f">{wuhan_ref.id}\n{wuhan_ref.seq}\n")
+        g.write(f"id\tdate\n{wuhan_ref.id}\t2019-12-29\n")
+        for row_idx, row in synthdata.iterrows():
+            for col_name, col in row.items():
+                # Fetch the row number, the column name and the entry in the synthdata
+                f.write(f">{col_name}_{row_idx}\n{create_synthetic_sequence(col, wuhan_ref)}\n")
+                g.write(f"{col_name}_{row_idx}\t{DATE_MAP[row_idx].strftime('%Y-%m-%d')}\n")
+
+def process_test5_files():
+    """Process all .txt files in test5 subdirectories and generate corresponding .fasta and .tsv files.
+    """
+    WUHAN_REF = get_wuhan_ref()
+
+    for subdir in os.listdir(TEST5_BASE_PATH):
+        txt_files = [
+            file
+            for file in os.listdir(f"{TEST5_BASE_PATH}/{subdir}")
+            if file.endswith(".txt")
+        ]
+
+        for txt_file in txt_files:
+        
+            name = txt_file.strip(".txt")
+            create_synthetic_sequences(
+                f"{TEST5_BASE_PATH}/{subdir}/{name}",
+                load_synthdata(
+                    f"{TEST5_BASE_PATH}/{subdir}/{txt_file}"
+                ),
+                WUHAN_REF
+            )
+        
+
+#´:°•.°+.*•´.*:˚.°*.˚•´.°:°•.°•.*•´.*:˚.°*.˚•´.°:°•.°+.*•´.*:#
+#                           MAIN                             #
+#.•°:°.´+˚.*°.˚:*.´•*.+°.•°:´*.´•*.•°.•°:°.´:•˚°.*°.˚:*.´+°.•#
+
+def main():
+    """Main function to process all test5 files.
+    """
+    print("Processing all .txt files in test5 subdirectories...")
+    process_test5_files()
+    print("All synthetic datasets created successfully.")
+
+if __name__ == "__main__":
+    main()