smftools 0.1.7__py3-none-any.whl → 0.2.1__py3-none-any.whl

smftools/informatics/helpers/plot_bed_histograms.py

@@ -0,0 +1,269 @@
+# plot_bed_histograms
+
+def plot_bed_histograms(bed_file, plotting_directory, fasta):
+    """
+    Plots read length, coverage, mapq, read quality stats for each record.
+
+    Parameters:
+        bed_file (str): Path to the bed file to derive metrics from.
+        plot_directory (str): Path to the directory to write out historgrams.
+        fasta (str): Path to FASTA corresponding to bed
+
+    Returns:
+        None
+    """
+    import pandas as pd
+    import matplotlib.pyplot as plt
+    import numpy as np
+    import os
+
+    # plot_bed_histograms.py
+
+def plot_bed_histograms(
+    bed_file,
+    plotting_directory,
+    fasta,
+    *,
+    bins=60,
+    clip_quantiles=(0.0, 0.995),
+    cov_bin_size=1000,       # coverage bin size in bp
+    rows_per_fig=6,          # paginate if many chromosomes
+    include_mapq_quality=True,   # add MAPQ + avg read quality columns to grid
+    coordinate_mode="one_based",  # "one_based" (your BED-like) or "zero_based"
+):
+    """
+    Plot per-chromosome QC grids from a BED-like file.
+
+    Expects columns:
+      chrom, start, end, read_len, qname, mapq, avg_base_qual
+
+    For each chromosome:
+      - Column 1: Read length histogram
+      - Column 2: Coverage across the chromosome (binned)
+      - (optional) Column 3: MAPQ histogram
+      - (optional) Column 4: Avg base quality histogram
+
+    The figure is paginated: rows = chromosomes (up to rows_per_fig), columns depend on include_mapq_quality.
+    Saves one PNG per page under `plotting_directory`.
+
+    Parameters
+    ----------
+    bed_file : str
+    plotting_directory : str
+    fasta : str
+        Reference FASTA (used to get chromosome lengths).
+    bins : int
+        Histogram bins for read length / MAPQ / quality.
+    clip_quantiles : (float, float)
+        Clip hist tails for readability (e.g., (0, 0.995)).
+    cov_bin_size : int
+        Bin size (bp) for coverage plot; bigger = faster/coarser.
+    rows_per_fig : int
+        Number of chromosomes per page.
+    include_mapq_quality : bool
+        If True, add MAPQ and avg base quality histograms as extra columns.
+    coordinate_mode : {"one_based","zero_based"}
+        One-based, inclusive (your file) vs BED-standard zero-based, half-open.
+    """
+    import os
+    import numpy as np
+    import pandas as pd
+    import matplotlib.pyplot as plt
+    import pysam
+
+    os.makedirs(plotting_directory, exist_ok=True)
+
+    bed_basename = os.path.basename(bed_file).rsplit(".bed", 1)[0]
+    print(f"[plot_bed_histograms] Loading: {bed_file}")
+
+    # Load BED-like table
+    cols = ['chrom', 'start', 'end', 'read_len', 'qname', 'mapq', 'avg_q']
+    df = pd.read_csv(bed_file, sep="\t", header=None, names=cols, dtype={
+        'chrom': str, 'start': int, 'end': int, 'read_len': int, 'qname': str,
+        'mapq': float, 'avg_q': float
+    })
+
+    # Drop unaligned records (chrom == '*') if present
+    df = df[df['chrom'] != '*'].copy()
+    if df.empty:
+        print("[plot_bed_histograms] No aligned reads found; nothing to plot.")
+        return
+
+    # Ensure coordinate mode consistent; convert to 0-based half-open for bin math internally
+    # Input is typically one_based inclusive (from your writer).
+    if coordinate_mode not in {"one_based", "zero_based"}:
+        raise ValueError("coordinate_mode must be 'one_based' or 'zero_based'")
+
+    if coordinate_mode == "one_based":
+        # convert to 0-based half-open [start0, end0)
+        start0 = df['start'].to_numpy() - 1
+        end0   = df['end'].to_numpy()   # inclusive in input -> +1 already handled by not subtracting
+    else:
+        # already 0-based half-open (assumption)
+        start0 = df['start'].to_numpy()
+        end0   = df['end'].to_numpy()
+
+    # Clip helper for hist tails
+    def _clip_series(s, q=(0.0, 0.995)):
+        if q is None:
+            return s.to_numpy()
+        lo = s.quantile(q[0]) if q[0] is not None else s.min()
+        hi = s.quantile(q[1]) if q[1] is not None else s.max()
+        x = s.to_numpy(dtype=float)
+        return np.clip(x, lo, hi)
+
+    # Load chromosome order/lengths from FASTA
+    with pysam.FastaFile(fasta) as fa:
+        ref_names = list(fa.references)
+        ref_lengths = dict(zip(ref_names, fa.lengths))
+
+    # Keep only chroms present in FASTA and with at least one read
+    chroms = [c for c in df['chrom'].unique() if c in ref_lengths]
+    # Order chromosomes by FASTA order
+    chrom_order = [c for c in ref_names if c in chroms]
+
+    if not chrom_order:
+        print("[plot_bed_histograms] No chromosomes from BED are present in FASTA; aborting.")
+        return
+
+    # Pagination
+    def _sanitize(name: str) -> str:
+        return "".join(ch if ch.isalnum() or ch in "-._" else "_" for ch in name)
+
+    cols_per_fig = 4 if include_mapq_quality else 2
+
+    for start_idx in range(0, len(chrom_order), rows_per_fig):
+        chunk = chrom_order[start_idx:start_idx + rows_per_fig]
+        nrows = len(chunk)
+        ncols = cols_per_fig
+
+        fig, axes = plt.subplots(
+            nrows=nrows, ncols=ncols,
+            figsize=(4.0 * ncols, 2.6 * nrows),
+            dpi=160,
+            squeeze=False
+        )
+
+        for r, chrom in enumerate(chunk):
+            chrom_len = ref_lengths[chrom]
+            mask = (df['chrom'].to_numpy() == chrom)
+
+            # Slice per-chrom arrays for speed
+            s0 = start0[mask]
+            e0 = end0[mask]
+            len_arr = df.loc[mask, 'read_len']
+            mapq_arr = df.loc[mask, 'mapq']
+            q_arr = df.loc[mask, 'avg_q']
+
+            # --- Col 1: Read length histogram (clipped) ---
+            ax = axes[r, 0]
+            ax.hist(_clip_series(len_arr, clip_quantiles), bins=bins, edgecolor="black", alpha=0.7)
+            if r == 0:
+                ax.set_title("Read length")
+            ax.set_ylabel(f"{chrom}\n(n={mask.sum()})")
+            ax.set_xlabel("bp")
+            ax.grid(alpha=0.25)
+
+            # --- Col 2: Coverage (binned over genome) ---
+            ax = axes[r, 1]
+            nb = max(1, int(np.ceil(chrom_len / cov_bin_size)))
+            # Bin edges in 0-based coords
+            edges = np.linspace(0, chrom_len, nb + 1, dtype=int)
+
+            # Compute per-bin "read count coverage": number of reads overlapping each bin.
+            # Approximate by incrementing all bins touched by the interval.
+            # (Fast and memory-light; for exact base coverage use smaller cov_bin_size.)
+            cov = np.zeros(nb, dtype=np.int32)
+            # bin indices overlapped by each read (0-based half-open)
+            b0 = np.minimum(np.searchsorted(edges, s0, side="right") - 1, nb - 1)
+            b1 = np.maximum(np.searchsorted(edges, np.maximum(e0 - 1, 0), side="right") - 1, 0)
+            # ensure valid ordering
+            b_lo = np.minimum(b0, b1)
+            b_hi = np.maximum(b0, b1)
+
+            # Increment all bins in range; loop but at bin resolution (fast for reasonable cov_bin_size).
+            for lo, hi in zip(b_lo, b_hi):
+                cov[lo:hi + 1] += 1
+
+            x_mid = (edges[:-1] + edges[1:]) / 2.0
+            ax.plot(x_mid, cov)
+            if r == 0:
+                ax.set_title(f"Coverage (~{cov_bin_size} bp bins)")
+            ax.set_xlim(0, chrom_len)
+            ax.set_xlabel("Position (bp)")
+            ax.set_ylabel("")  # already show chrom on col 1
+            ax.grid(alpha=0.25)
+
+            if include_mapq_quality:
+                # --- Col 3: MAPQ ---
+                ax = axes[r, 2]
+                # Clip MAPQ upper tail if needed (usually 60)
+                ax.hist(_clip_series(mapq_arr.fillna(0), clip_quantiles), bins=bins, edgecolor="black", alpha=0.7)
+                if r == 0:
+                    ax.set_title("MAPQ")
+                ax.set_xlabel("MAPQ")
+                ax.grid(alpha=0.25)
+
+                # --- Col 4: Avg base quality ---
+                ax = axes[r, 3]
+                ax.hist(_clip_series(q_arr.fillna(np.nan), clip_quantiles), bins=bins, edgecolor="black", alpha=0.7)
+                if r == 0:
+                    ax.set_title("Avg base qual")
+                ax.set_xlabel("Phred")
+                ax.grid(alpha=0.25)
+
+        fig.suptitle(
+            f"{bed_basename} — per-chromosome QC "
+            f"({'len,cov,MAPQ,qual' if include_mapq_quality else 'len,cov'})",
+            y=0.995, fontsize=11
+        )
+        fig.tight_layout(rect=[0, 0, 1, 0.98])
+
+        page = start_idx // rows_per_fig + 1
+        out_png = os.path.join(plotting_directory, f"{_sanitize(bed_basename)}_qc_page{page}.png")
+        plt.savefig(out_png, bbox_inches="tight")
+        plt.close(fig)
+
+    print("[plot_bed_histograms] Done.")
+
+
+    # bed_basename = os.path.basename(bed_file).split('.bed')[0]
+    # # Load the BED file into a DataFrame
+    # print(f"Loading BED to plot read length and coverage histograms: {bed_file}")
+    # df = pd.read_csv(bed_file, sep='\t', header=None, names=['chromosome', 'start', 'end', 'length', 'read_name', 'mapq', 'read_quality'])
+    
+    # # Group by chromosome
+    # grouped = df.groupby('chromosome')
+
+    # # for each chromosome, get the record length of that chromosome from the fasta. Use from 0 to this length for the positional coverage plot.
+
+    # # Change below and make a plot grid instead. For each, make row for chromsome, col for read length and coverage
+    # # Clip the outliers to make plots cleaner
+
+    # for chrom, group in grouped:
+    #     # Plot read length histogram
+    #     plt.figure(figsize=(12, 6))
+    #     plt.hist(group['length'], bins=50, edgecolor='k', alpha=0.7)
+    #     plt.title(f'Read Length Histogram of reads aligned to {chrom}')
+    #     plt.xlabel('Read Length')
+    #     plt.ylabel('Count')
+    #     plt.grid(True)
+    #     save_name = os.path.join(plotting_directory, f'{bed_basename}_{chrom}_read_length_histogram.png')
+    #     plt.savefig(save_name)
+    #     plt.close()
+
+    #     # Compute coverage
+    #     coverage = np.zeros(group['end'].max())
+    #     for _, row in group.iterrows():
+    #         coverage[row['start']:row['end']] += 1
+        
+    #     # Plot coverage histogram
+    #     plt.figure(figsize=(12, 6))
+    #     plt.plot(coverage, color='b')
+    #     plt.title(f'Coverage Histogram for {chrom}')
+    #     plt.xlabel('Position')
+    #     plt.ylabel('Coverage')
+    #     plt.grid(True)
+    #     save_name = os.path.join(plotting_directory, f'{bed_basename}_{chrom}_coverage_histogram.png')
+    #     plt.savefig(save_name)
+    #     plt.close()

smftools/informatics/helpers/separate_bam_by_bc.py

@@ -1,6 +1,5 @@
 ## separate_bam_by_bc
 
-# General
 def separate_bam_by_bc(input_bam, output_prefix, bam_suffix, split_dir):
     """
     Separates an input BAM file on the BC SAM tag values.
@@ -29,7 +28,8 @@ def separate_bam_by_bc(input_bam, output_prefix, bam_suffix, split_dir):
         for read in bam:
             try:
                 # Get the barcode tag value
-                bc_tag = read.get_tag("BC", with_value_type=True)[0].split('barcode')[1]
+                bc_tag = read.get_tag("BC", with_value_type=True)[0]
+                #bc_tag = read.get_tag("BC", with_value_type=True)[0].split('barcode')[1]
                 # Open the output BAM file corresponding to the barcode
                 if bc_tag not in output_files:
                     output_path = os.path.join(split_dir, f"{output_prefix}_{bam_base_minus_suffix}_{bc_tag}{bam_suffix}")

smftools/informatics/helpers/split_and_index_BAM.py

@@ -1,13 +1,12 @@
 ## split_and_index_BAM
 
-def split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix, output_directory):
+def split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix):
     """
     A wrapper function for splitting BAMS and indexing them.
     Parameters:
         aligned_sorted_BAM (str): A string representing the file path of the aligned_sorted BAM file.
         split_dir (str): A string representing the file path to the directory to split the BAMs into.
         bam_suffix (str): A suffix to add to the bam file.
-        output_directory (str): A file path to the directory to output all the analyses.
     
     Returns:
         None
@@ -20,9 +19,6 @@ def split_and_index_BAM(aligned_sorted_BAM, split_dir, bam_suffix, output_direct
     from .separate_bam_by_bc import separate_bam_by_bc
     from .make_dirs import make_dirs
 
-    plotting_dir = os.path.join(output_directory, 'demultiplexed_bed_histograms')
-    bed_dir = os.path.join(output_directory, 'demultiplexed_read_alignment_coordinates')
-    make_dirs([plotting_dir, bed_dir])
     aligned_sorted_output = aligned_sorted_BAM + bam_suffix
     file_prefix = readwrite.date_string()
     separate_bam_by_bc(aligned_sorted_output, file_prefix, bam_suffix, split_dir)