Merge pull request #551 from shiridikumar/main

updated random DNA/RNA sequence generator

PAMI/extras/syntheticDataGenerator/createSyntheticNucleotideSequence.py

@@ -0,0 +1,94 @@
+import random
+import time
+import psutil
+import os
+
+class NucleotideSequenceGenerator:
+    """
+    :Description: NucleotideSequenceGenerator generates a random DNA or RNA sequence with specified GC content and length.
+    :Attributes:
+        sequence_length: int
+            Length of the generated sequence.
+        gc_content: float
+            Desired GC content as a decimal (e.g., 0.5 for 50%).
+        is_rna: bool
+            True for RNA sequence, False for DNA sequence.
+        sequence: str
+            Generated DNA or RNA sequence.
+        memoryUSS : float
+            Stores the total amount of USS memory consumed by the program.
+        memoryRSS : float
+            Stores the total amount of RSS memory consumed by the program.
+        startTime : float
+            Records the start time of the sequence generation process.
+        endTime : float
+            Records the completion time of the sequence generation process.
+    :Methods:
+        create:
+            Generates the random DNA or RNA sequence.
+        save:
+            Saves the generated sequence to a user-specified file.
+        getSequence:
+            Returns the generated sequence.
+        getMemoryUSS:
+            Retrieves the total amount of USS memory consumed by the process.
+        getMemoryRSS:
+            Retrieves the total amount of RSS memory consumed by the process.
+        getRuntime:
+            Retrieves the total runtime taken by the sequence generation process.
+    """
+
+    def __init__(self, sequence_length, gc_content, is_rna=False):
+        self.sequence_length = sequence_length
+        self.gc_content = gc_content
+        self.is_rna = is_rna
+        self.sequence = ""
+        self._startTime = float()
+        self._endTime = float()
+        self._memoryUSS = float()
+        self._memoryRSS = float()
+
+    def create(self):
+        self._startTime = time.time()
+
+        # Define nucleotide choices based on DNA or RNA
+        nucleotides = "GCAU" if self.is_rna else "GCAT"
+
+        # Calculate number of G/C and A/T (or A/U) bases
+        gc_count = int(self.sequence_length * self.gc_content)
+        at_count = self.sequence_length - gc_count
+
+        # Build the sequence with the correct proportion of GC and AT
+        sequence_list = (
+            random.choices("GC", k=gc_count) +
+            random.choices("AU" if self.is_rna else "AT", k=at_count)
+        )
+
+        # Shuffle to randomize order
+        random.shuffle(sequence_list)
+
+        # Convert list to string
+        self.sequence = "".join(sequence_list)
+
+        self._endTime = time.time()
+
+    def save(self, filename):
+        with open(filename, 'w') as file:
+            file.write(self.sequence)
+
+    def getSequence(self):
+        return self.sequence
+
+    def getMemoryUSS(self) -> float:
+        process = psutil.Process(os.getpid())
+        self._memoryUSS = process.memory_full_info().uss
+        return self._memoryUSS
+
+    def getMemoryRSS(self) -> float:
+        process = psutil.Process(os.getpid())
+        self._memoryRSS = process.memory_info().rss
+        return self._memoryRSS
+
+    def getRuntime(self) -> float:
+        return self._endTime - self._startTime
+