Python Bio Pandas

Pandas for Bioinformatics

When to Use

• Selecting or filtering rows/columns of a gene table, count matrix, or clinical sheet by label (.loc) or position (.iloc).
• Merging expression data with a gene annotation or sample metadata table and needing to catch genes that don't match.
• Computing per-group statistics — mean expression per condition, per-gene z-score within a group — with groupby.
• Loading a count matrix or sample sheet from CSV/TSV (counts.csv, GEO-style series matrix, BED/GTF attribute exports).
• Reshaping a genes × samples wide table into long format for plotting or statistical modeling.

Version Compatibility

pandas ≥2.0, NumPy ≥1.24, Python ≥3.10. pandas ≥2.0 defaults to stricter chained-assignment warnings (copy-on-write is opt-in via pd.options.mode.copy_on_write = True pre-3.0, default from pandas 3.0) — the .loc[mask, col] = val pattern below is safe under both.

Prerequisites

pip install pandas numpy. Assumes basic Python (dict/list comprehension) and familiarity with what a gene expression count matrix looks like (genes × samples). For array-level math (RPKM/CPM, PWMs, broadcasting) see python-bio-numpy; for cleaning/reshaping beyond what's here see python-bio-data-wrangling.

Complicated Moments

loc vs iloc vs []: df['col'] selects a column. df.loc[row_label, col_label] selects by label. df.iloc[row_int, col_int] selects by integer position. After filtering, integer positions no longer match original labels — always know which accessor you need.

Chain indexing creates copies unpredictably: df[df['gc'] > 0.5]['length'] = 100 may silently fail to modify df. Always use df.loc[mask, 'length'] = 100.

groupby + transform vs agg: agg reduces each group to one row. transform returns a same-shape Series aligned to the original index, each row filled with its group's statistic — this is what you want for group-wise normalization added back as a new column.

Left join for annotation merges: merge(..., how='inner') silently drops genes missing from the annotation table. Default to how='left' and inspect the resulting NaNs.

Selecting and Filtering

Goal: pull rows/columns out of a gene table by label, position, or condition, without falling into the chained-assignment trap. Approach: use .loc for label-based access and safe assignment, .iloc for positional access, boolean masks or .query() for filtering.

import pandas as pd

genes_df = pd.DataFrame({
    'gene': ['BRCA1', 'TP53', 'EGFR', 'MYC', 'KRAS'],
    'chromosome': ['17', '17', '7', '8', '12'],
    'length_bp': [7088, 2512, 5616, 2357, 5764],
    'gc_content': [0.423, 0.512, 0.487, 0.551, 0.448],
})


def flag_long_gc_rich(df, length_thresh=5000, gc_thresh=0.45):
    """Return a copy of df with a boolean 'long_gc_rich' column.

    Uses .loc for the assignment so it never triggers a
    SettingWithCopyWarning / silent no-op on a filtered copy.
    """
    df = df.copy()
    mask = (df['length_bp'] > length_thresh) & (df['gc_content'] > gc_thresh)
    df.loc[mask, 'long_gc_rich'] = True
    df['long_gc_rich'] = df['long_gc_rich'].fillna(False)
    return df


flagged = flag_long_gc_rich(genes_df)

# label vs position access
genes_df.loc[0, 'gene']            # by label -> 'BRCA1'
genes_df.iloc[0, 0]                # by integer position -> 'BRCA1'
genes_df.loc[1:3, ['gene', 'length_bp']]   # label slice is INCLUSIVE of end

# readable filtering with .query() (equivalent to the boolean-mask version)
chr17_gc_rich = genes_df.query('chromosome == "17" and gc_content > 0.45')

Annotation Merges

Goal: attach gene/sample metadata to an expression table without silently dropping unmatched rows. Approach: always start with how='left', then count NaNs introduced by the merge before deciding whether to drop or investigate them.

def merge_with_annotation(expr_df, annotation_df, on='gene_id'):
    """Left-join expression data with an annotation table and report misses.

    Left join keeps every row of expr_df; genes absent from annotation_df
    get NaN annotation columns instead of being silently dropped (as an
    inner join would do).
    """
    merged = expr_df.merge(annotation_df, on=on, how='left')
    n_missing = merged['gene_name'].isna().sum()
    if n_missing:
        print(f"Warning: {n_missing} genes missing annotation")
    return merged

GroupBy: agg vs transform

Goal: compute per-condition summary statistics, and separately, per-condition normalized values that stay aligned to the original rows. Approach: agg for one-row-per-group summaries, transform for same-shape group-wise normalization.

import numpy as np

df = pd.DataFrame({
    'gene': [f'Gene_{i}' for i in range(6)],
    'condition': ['ctrl', 'ctrl', 'ctrl', 'treat', 'treat', 'treat'],
    'expression': [120.0, 45.0, 300.0, 340.0, 44.0, 310.0],
})

# agg: one row per group
summary = df.groupby('condition', as_index=False).agg(
    mean_expr=('expression', 'mean'),
    n=('expression', 'count'),
)

# transform: same shape as input, each row filled with its group's z-score
df['expr_zscore'] = df.groupby('condition')['expression'].transform(
    lambda x: (x - x.mean()) / x.std()
)

Reading Expression Data

# Count matrix: genes as row index, one column per sample
counts = pd.read_csv('counts.csv', index_col=0)

# TSV (common for BED/GTF attribute exports)
metadata = pd.read_csv('samples.tsv', sep='\t')

# Wide (genes x samples) -> long (one row per gene x sample observation)
long = counts.reset_index().melt(
    id_vars='gene_id', var_name='sample', value_name='count'
)

Pitfalls

• Chain indexing: df[mask]['col'] = val sets a copy silently. Use df.loc[mask, 'col'] = val.
• groupby index: by default the grouping key becomes the index; use as_index=False to keep it as a column.
• Integer index after filtering: after df = df[df['qc_pass']], df.iloc[0] is the first remaining row but df.loc[0] still refers to original label 0 (may raise KeyError). Call df.reset_index(drop=True) if you need position-based access afterward.
• .loc slices are inclusive: df.loc[1:3] includes row label 3, unlike df.iloc[1:3] or a Python list slice.
• Inner-join data loss: merge(..., how='inner') on an incomplete annotation table drops genes with no match instead of flagging them — default to how='left'.
• np.log2 on zero counts: add a pseudocount (+ 1) before log-transforming raw read counts; pandas won't warn you about -inf.

See Also

• python-bio-numpy — vectorized array math (RPKM/CPM, PWMs, broadcasting) underlying pandas columns.
• python-bio-data-wrangling — cleaning (NaN imputation, dedup, type coercion) and wide/long reshaping beyond basic melt.
• bio-expression-matrix-counts-ingest — loading raw count matrices from GEO/featureCounts/salmon output.
• bio-expression-matrix-gene-id-mapping — normalizing gene identifiers before merging annotation tables.