Added Markov process script.

Author: keshav-gandhi

neat/models/markov.py

@@ -0,0 +1,143 @@
+import pysam
+import numpy as np
+import pandas as pd
+import pathlib
+import matplotlib.pyplot as plt
+import seaborn as sns
+from scipy.stats import norm
+
+def make_qual_score_list(bam_file):
+    '''Takes an input BAM file and creates lists of quality scores. This becomes a data frame, which will be
+    pre-processed for Markov chain analysis.'''
+
+    index = f'{bam_file}.bai'
+
+    if not pathlib.Path(index).exists():
+        print('No index found, creating one.')
+
+        pysam.index(bam_file)
+
+    file_to_parse = pysam.AlignmentFile(bam_file, 'rb', check_sq=False)
+    num_recs = file_to_parse.count()
+    print(f'{num_recs} records to parse')
+
+    modulo = round(num_recs / 9)
+
+    qual_list = []
+    i = 0
+    j = 0
+
+    def print_update(number, factor, percent):
+        if number % factor == 0:
+            percent += 10
+            print(f'{percent}% complete', end='\r')
+        return percent
+
+    print('Parsing file')
+
+    for item in file_to_parse.fetch():
+        if item.is_unmapped or len(item.seq) != 249 or 'S' in item.cigarstring:
+            i += 1
+            j = print_update(i, modulo, j)
+            continue
+
+        # Mapping quality scores
+
+        align_qual = item.query_alignment_qualities
+
+        # Append to master lists
+
+        qual_list.append(align_qual)
+        i += 1
+        j = print_update(i, modulo, j)
+
+    print(f'100% complete')
+    file_to_parse.close()
+
+    # Turn list of lists into a dataframe
+
+    quality_df = pd.DataFrame(qual_list)
+
+    # Pre-processing - fill in missing data and sample 1% of reads
+
+    quality_df = quality_df.fillna(0)
+    quality_df = quality_df.sample(frac=0.01, axis=0, random_state=42)
+
+    return quality_df
+
+def estimate_transition_probabilities():
+
+    # Define the probabilities for transition states based on a normal distribution
+
+    std_dev = 1
+    transition_probs = {
+        -3: norm.pdf(-3, 0, std_dev),
+        -2: norm.pdf(-2, 0, std_dev),
+        -1: norm.pdf(-1, 0, std_dev),
+        0: norm.pdf(0, 0, std_dev),
+        1: norm.pdf(1, 0, std_dev),
+        2: norm.pdf(2, 0, std_dev),
+        3: norm.pdf(3, 0, std_dev)
+    }
+
+    # Normalize the probabilities to sum to 1
+
+    total_prob = sum(transition_probs.values())
+    for k in transition_probs:
+        transition_probs[k] /= total_prob
+
+    return transition_probs
+
+def apply_markov_chain(quality_df, L=249):
+    
+    transition_probs = estimate_transition_probabilities()
+    num_rows, num_cols = quality_df.shape
+
+    markov_preds = []
+
+    for row in quality_df.iterrows():
+        qualities = row[1].values
+        pred_qualities = np.zeros_like(qualities)
+        pred_qualities[0] = qualities[0] # initial state
+ 
+        for i in range(1, L):
+            prev_quality = pred_qualities[i - 1]
+            transitions = list(transition_probs.keys())
+            probabilities = list(transition_probs.values())
+            next_quality = np.random.choice(transitions, p=probabilities)
+            pred_qualities[i] = max(0, prev_quality + next_quality) # ensuring no negative qualities
+
+        markov_preds.append(pred_qualities)
+
+    markov_preds_df = pd.DataFrame(markov_preds)
+
+    # Apply final transformations
+
+    edge_len = int(L * 0.05)
+    mid_start = int(L * 0.40)
+    mid_end = int(L * 0.60)
+
+    markov_preds_df.iloc[:, :edge_len] -= 5
+    markov_preds_df.iloc[:, :edge_len] = markov_preds_df.iloc[:, :edge_len].clip(lower=0)
+
+    markov_preds_df.iloc[:, -edge_len:] -= 5
+    markov_preds_df.iloc[:, -edge_len:] = markov_preds_df.iloc[:, -edge_len:].clip(lower=0)
+
+    markov_preds_df.iloc[:, mid_start:mid_end] += 1
+
+    return markov_preds_df
+
+def plot_heatmap(y_preds_df, file_path):
+    '''Takes a dataframe of predicted quality scores and plots a seaborn heatmap to visualize them.'''
+
+    sns.heatmap(y_preds_df, vmin=0, vmax=40, cmap='viridis')
+    plt.savefig(file_path)
+    print('Heatmap plotted')
+
+# Example usage
+
+bam_file = '/projects/bclt/neat_data/H1N1_new.bam'
+test_df = make_qual_score_list(bam_file)
+markov_preds_df = apply_markov_chain(test_df)
+plot_heatmap(markov_preds_df, 'markov_chain_heatmap.svg')
+