Analyze PacBio CCSs

This notebook analyzes the PacBio CCSs that have been previously aligned and parsed with alignparse.

Import Python modules:

import os

import alignparse.targets

import altair as alt

import pandas as pd

import yaml

Get configuration information:

# If you are running notebook interactively rather than in pipeline that handles
# working directories, you may have to first `os.chdir` to appropriate directory.

with open("config.yaml") as f:
    config = yaml.safe_load(f)

Read in the PacBio runs:

pacbio_runs = (
    pd.read_csv(config["pacbio_runs"])
    .assign(
        pacbioRun=lambda x: x["library"] + "_" + x["run"].astype(str),
        subdir=lambda x: config["process_ccs_dir"] + "/" + x["pacbioRun"],
    )
    .drop(columns="fastq")
)

pacbio_runs

	library	run	pacbioRun	subdir
0	Lib-1	211105	Lib-1_211105	results/process_ccs/Lib-1_211105
1	Lib-3	211105	Lib-3_211105	results/process_ccs/Lib-3_211105
2	Lib-2	211105	Lib-2_211105	results/process_ccs/Lib-2_211105
3	Lib-4	211105	Lib-4_211105	results/process_ccs/Lib-4_211105
4	Lib-1	220124	Lib-1_220124	results/process_ccs/Lib-1_220124
5	Lib-3	220124	Lib-3_220124	results/process_ccs/Lib-3_220124
6	Lib-2	220124	Lib-2_220124	results/process_ccs/Lib-2_220124
7	Lib-4	220124	Lib-4_220124	results/process_ccs/Lib-4_220124

Stats on CCS alignments

Read and plot the alignment stats from running alignparse on the PacBio CCSs:

readstats = pd.concat(
    [
        (
            pd.read_csv(os.path.join(row.subdir, "readstats.csv")).assign(
                pacbioRun=row.pacbioRun, library=row.library
            )
        )
        for row in pacbio_runs.itertuples()
    ],
    ignore_index=True,
)

readstats_chart = (
    alt.Chart(readstats)
    .encode(
        x="count:Q",
        y=alt.Y(
            "category:N",
            axis=alt.Axis(title=None),
        ),
        tooltip=readstats.columns.tolist(),
        facet=alt.Facet("pacbioRun:N", columns=2, title=None),
    )
    .mark_bar()
    .properties(width=250, height=75)
    .resolve_scale(x="independent", y="independent")
)

readstats_chart

/fh/fast/bloom_j/computational_notebooks/jbloom/2022/SARS-CoV-2_Delta_spike_DMS/.snakemake/conda/ca86f4d86d6bb2d089b489af720dfeeb/lib/python3.9/site-packages/altair/utils/core.py:317: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for col_name, dtype in df.dtypes.iteritems():

Visualize target to which reads are being aligned

Draw images of the target we’re parsing:

targets = alignparse.targets.Targets(
    seqsfile=config["pacbio_amplicon"],
    feature_parse_specs=config["pacbio_amplicon_specs"],
)

fig = targets.plot(
    ax_width=7,
    plots_indexing="genbank",
    ax_height=2,
    hspace=1.2,
)

Why were some CCSs filtered?

Plot the number of CCSs filtered for each reason:

# CSVs holding filtered reads
filtered_csvs = pd.concat(
    [
        (
            pd.read_csv(os.path.join(row.subdir, "filtered.csv")).assign(
                pacbioRun=row.pacbioRun, library=row.library
            )
        )
        for row in pacbio_runs.itertuples()
    ],
    ignore_index=True,
)

# details for all filtered reads
filtered = pd.concat(
    [
        pd.read_csv(row.csv_file).assign(
            target=row.target, pacbioRun=row.pacbioRun, library=row.library
        )
        for row in filtered_csvs.itertuples()
    ],
    ignore_index=True,
)

# count reasons for filtering, then add number of non-filtered
filtered_reasons = pd.concat(
    [
        filtered.groupby(["pacbioRun", "filter_reason"], as_index=False).aggregate(
            count=pd.NamedAgg("query_name", "count")
        ),
        readstats.query('category.str.startswith("aligned")', engine="python")
        .groupby("pacbioRun", as_index=False)
        .aggregate({"count": "sum"})
        .assign(filter_reason="aligned"),
    ]
).assign(
    total_counts=lambda x: x.groupby("pacbioRun")["count"].transform("sum"),
    frac_counts=lambda x: x["count"] / x["total_counts"],
)

# make chart
filtered_chart = (
    alt.Chart(filtered_reasons)
    .encode(
        x="count:Q",
        y=alt.Y(
            "filter_reason:N",
            axis=alt.Axis(title=None),
        ),
        color="is_aligned:N",
        tooltip=filtered_reasons.columns.tolist(),
        facet=alt.Facet("pacbioRun:N", columns=2, title=None),
    )
    .mark_bar()
    .properties(width=250, height=75)
    .resolve_scale(x="independent", y="independent")
    .transform_filter(alt.datum.frac_counts > 0.01)
    .transform_calculate(is_aligned=alt.datum.filter_reason == "aligned")
)

filtered_chart

/fh/fast/bloom_j/computational_notebooks/jbloom/2022/SARS-CoV-2_Delta_spike_DMS/.snakemake/conda/ca86f4d86d6bb2d089b489af720dfeeb/lib/python3.9/site-packages/altair/utils/core.py:317: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  for col_name, dtype in df.dtypes.iteritems():

Get CCSs that align to the amplicon

# CSVs holding aligned reads
aligned_csvs = pd.concat(
    [
        (
            pd.read_csv(os.path.join(row.subdir, "aligned.csv")).assign(
                pacbioRun=row.pacbioRun, library=row.library
            )
        )
        for row in pacbio_runs.itertuples()
    ],
    ignore_index=True,
)

assert aligned_csvs["target"].nunique() == 1

aligned = pd.concat(
    [
        (
            pd.read_csv(row.csv_file)
            .assign(pacbioRun=row.pacbioRun, library=row.library)
            .drop(columns=["query_clip5", "query_clip3"])
            .rename(columns={"barcode_sequence": "barcode"})
        )
        for row in aligned_csvs.itertuples()
    ],
    ignore_index=True,
)
print(f"\nRead {len(aligned):.4g} alignable CCSs:")
display(
    aligned.groupby("pacbioRun").aggregate(n_CCSs=pd.NamedAgg("query_name", "count"))
)
output_csv = config["aligned_ccs_file"]
print(f"Writing to {output_csv}")
aligned.to_csv(output_csv, index=False)

Read 3.531e+06 alignable CCSs:

	n_CCSs
pacbioRun
Lib-1_211105	555551
Lib-1_220124	576055
Lib-2_211105	442826
Lib-2_220124	455196
Lib-3_211105	277734
Lib-3_220124	286468
Lib-4_211105	461149
Lib-4_220124	475648

Writing to results/process_ccs/CCSs_aligned_to_amplicon.csv