Issue 7

src/read_sequencing.py

+"""Read Sequencing.
+
+Simulate the sequencing of reads on the template of terminal fragments and simulates reads of these fragments.
+Author: Kathleen Moriarty
+"""
+# Imports from built-in modules
+from random import choices
+from typing import List
+from pathlib import Path
+
+
+def read_sequencing(
+    frag_file_name: Path,
+    output_file_name: Path = Path.cwd() / 'output_reads.txt',
+    num_reads: int = 1000,
+    read_len: int = 80,
+) -> None:
+    """Reads a fasta-formatted file of terminal fragments and simulates reads.
+
+    Simulate the sequencing of reads on the template of terminal
+    fragments. Reads are copies of fixed length starting
+    from the 5' end of fragments. If the desired read length
+    is larger than the fragment length, sequencing would in
+    principle proceed into the 3' adaptor and then would perhaps
+    yield random bases. For simplicity, here we assume that random
+    nucleotides are introduced in this case. Saves a fasta-formatted
+    file of reads of identical length, representing 5’
+    ends of the terminal fragments as .txt.
+
+    Args:
+        frag_file_name: input file path of terminal fragments
+        output_file_name: output file path where to store the output
+        num_reads: number of total reads to simulate
+        read_len: integer of identical read length
+    """
+    # Read data from terminal fragment file
+    # Store fragment descriptions in a list
+    frag_desc = []  # type: List[str]
+
+    with open(frag_file_name, 'r') as f:
+        frag_line = f.readline()
+        # Store all fragments as a list to parse later
+        frag_list = []  # type: List[str]
+        # Store combined fragment lines
+        frag_str = ""
+        while frag_line != "":
+            # To stop when the end of file is reached
+            if frag_line.startswith('>'):
+                # Determine if this is the first fragment in the file
+                # Ignore the description line (starting with >) of the first fragment
+                if not (len(frag_list) == 0 and frag_str == ""):
+                    # Not the first fragment. Append to list.
+                    frag_list.append(frag_str)
+                frag_str = ""
+                # Store description line for output file
+                frag_desc.append(frag_line)
+            else:
+                frag_str = frag_str + frag_line.rstrip("\n")
+            # Read next line
+            frag_line = f.readline()
+        frag_list.append(frag_str)
+
+    # Store list of random nucleotides from which to sample when read length is too short
+    nucleotides = ['A', 'C', 'G', 'T']
+
+    # Calculate sum of all lengths to determine the relative abundance for that fragment
+    sum_frags = sum(map(len, frag_list))
+
+    # Open the file to save the reads
+    with open(output_file_name, 'w') as fw:
+
+        # Loop through fasta fragments that start with 5'
+        for frag in frag_list:
+            # Determine number of reads to create from this fragment
+            # This might not always provide an exact number of reads that were asked
+            # TODO resolve this issue
+            num_frag_reads = round((len(frag)/sum_frags) * num_reads)
+
+            for i in range(0, num_frag_reads):
+                # If the read length is less than the required length given by the parameter,
+                # then add random nucleotides
+                if len(frag) < read_len:
+
+                    # Calculate number of random nucleotides to add to the end of the read
+                    diff = read_len - len(frag)
+
+                    # Select random nucleotides from list of possible
+                    rand_samp = choices(nucleotides, k=diff)
+
+                    # Add the random list to the read and save
+                    tmp_read = frag[0:len(frag)] + ''.join(rand_samp)
+                else:
+                    # Save subset of fragment as read
+                    tmp_read = frag[0:read_len]
+
+                # Write read to file and original fragment description
+                fw.write(frag_desc[frag_list.index(frag)])
+                fw.write(tmp_read + "\n\n")