pysam

Files (14)

• SKILL.md
• alignment_files.md · references/
• api_reference.md · references/
• common_workflows.md · references/
• coordinates_and_indexing.md · references/
• cram_and_performance.md · references/
• migration_to_0_24.md · references/
• sequence_files.md · references/
• sources.md · references/
• variant_files.md · references/
• alignment_qc.py · scripts/
• filter_alignments.py · scripts/
• inspect_hts.py · scripts/
• variant_summary.py · scripts/

SKILL.md (first lines)

# pysam

## Overview

Use pysam for low-level, streaming access to HTSlib-supported genomic formats:

- `AlignmentFile` and `AlignedSegment` for SAM/BAM/CRAM
- `VariantFile`, `VariantHeader`, and `VariantRecord` for VCF/BCF
- `FastaFile` for indexed FASTA and `FastxFile` for sequential FASTA/FASTQ
- `TabixFile` for BGZF-compressed, tabix-indexed BED/GFF/GTF/custom tables
- `pysam.samtools` and `pysam.bcftools` for wrapped command dispatchers

Current upstream baseline: **pysam 0.24.1** (7 September 2026), wrapping
HTSlib/samtools/bcftools 1.24. Read `references/sources.md` before updating
version-specific guidance.

## Installation

Use the pinned release for reproducible work:

```bash
uv pip install "pysam==0.24.1"
```

Confirm the runtime:

```python
import pysam

print(pysam.__version__)           # 0.24.1
print(pysam.__samtools_version__)  # 1.24
```

Prebuilt wheels are available for supported macOS and Linux platforms. A
source build needs a C compiler and HTSlib build dependencies; read the
official installation guide linked from `references/sources.md`.

## First Decide

Before writing code:

1. Identify the real format, compression, sort order, and available index.
2. Decide whether coordinates are numeric Python coordinates or a region
   string. Do not mix them.
3. For CRAM, identify the exact reference assembly and FASTA.
4. Prefer indexed region access; use sequential iteration only when intended.
5. Preserve headers when writing and write to a new path by default.
6. State filtering semantics: mapping/base quality, flags, overlap handling,
   duplicate handling, and pileup depth cap.

For unfamiliar files, start with the bundled read-only inspector:

```bash
python scripts/inspect_hts.py sample.bam
python scripts/inspect_hts.py cohort.vcf.gz
python scripts/inspect_hts.py reference.fa
```

## Bundled Scripts

| Script | Purpose | Typical call |
|---|---|---|
| `scripts/inspect_hts.py` | Metadata-only inspection for alignment, variant, FASTA, FASTQ, and tabix files | `python scripts/inspect_hts.py sample.cram --reference ref.fa` |
| `scripts/alignment_qc.py` | Streaming aggregate read/QC counts as JSON | `python scripts/alignment_qc.py sample.bam --max-records 100000` |
| `scripts/variant_summary.py` | Streaming variant, FILTER, and genotype summary as JSON | `python scripts/variant_summary.py cohort.vcf.gz --region chr1:1-1000000` |
| `scripts/filter_alignments.py` | Filter SAM/BAM/CRAM without changing record order | `python scripts/filter_alignments.py input.bam output.bam --exclude-secondary` |

All scripts refuse to overwrite existing outputs. The filter also refuses stale
output indexes and offers `--index --csi` for large BAM contigs. FASTA inspection
requires an existing `.fai`; create it explicitly with `pysam.faidx()` first.
Run each with `--help` for coordinate, index, and privacy notes.

Examples use illustrative filenames and assay-specific thresholds. The local
synthetic suite exercises these API patterns on pysam 0.24.1; remote storage and
biological datasets are not part of that validation.

## Coordinate Contract

**Numeric coordinates accepted by pysam APIs are 0-based, half-open.** This
includes numeric `AlignmentFile.fetch()`, `VariantFile.fetch()`,
`FastaFile.fetch()`, `TabixFile.fetch()`, and `pileup()` arguments.

**Region strings are samtools-style: 1-based and inclusive.**

```python
# The same 100 bases:
bam.fetch("chr1", 99, 199)          # [99, 199)
bam.fetch(region="chr1:100-199")    # 1-based inclusive
```

VCF text uses 1-based `POS`, while record properties expose both systems:

```python
record.pos    # 1-based
record.start  # 0-based inclusive
record.stop   # 0-based exclusive
```

Read `references/coordinates_and_indexing.md` for format conversions, overlap
semantics, index choices, and contig-name checks.

## Alignment Files

Use context managers and explicit modes:

```python
import pysam

with pysam.AlignmentFile("sample.bam", "rb", threads=4) as bam:
    for read in bam.fetch("chr1", 1_000, 2_000):
        if (
            not read.is_unmapped
            and not read.is_secondary
            and not read.is_supplementary
            and read.mapping_quality >= 30
        ):
            print(read.query_name, read.reference_start, read.cigarstring)
```

From K-Dense-AI/scientific-agent-skills, MIT.

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