pysam

Name: pysam
Author: LeonChaoX

698stars61forks

How to install pysam?

leonchaox/qinyan-academic-skills/pysam

$npx -y skills add LeonChaoX/qinyan-academic-skills --skill pysam

Installs into the current project.

Summary

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Files · 1

View on GitHub

SKILL.md

1	# Pysam
2
3	## Overview
4
5	Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.
6
7	## When to Use This Skill
8
9	This skill should be used when:
10	- Working with sequencing alignment files (BAM/CRAM)
11	- Analyzing genetic variants (VCF/BCF)
12	- Extracting reference sequences or gene regions
13	- Processing raw sequencing data (FASTQ)
14	- Calculating coverage or read depth
15	- Implementing bioinformatics analysis pipelines
16	- Quality control of sequencing data
17	- Variant calling and annotation workflows
18
19	## Quick Start
20
21	### Installation
22	```bash
23	uv pip install pysam
24	```
25
26	### Basic Examples
27
28	Read alignment file:
29	```python
30	import pysam
31
32	# Open BAM file and fetch reads in region
33	samfile = pysam.AlignmentFile("example.bam", "rb")
34	for read in samfile.fetch("chr1", 1000, 2000):
35	print(f"{read.query_name}: {read.reference_start}")
36	samfile.close()
37	```
38
39	Read variant file:
40	```python
41	# Open VCF file and iterate variants
42	vcf = pysam.VariantFile("variants.vcf")
43	for variant in vcf:
44	print(f"{variant.chrom}:{variant.pos} {variant.ref}>{variant.alts}")
45	vcf.close()
46	```
47
48	Query reference sequence:
49	```python
50	# Open FASTA and extract sequence
51	fasta = pysam.FastaFile("reference.fasta")
52	sequence = fasta.fetch("chr1", 1000, 2000)
53	print(sequence)
54	fasta.close()
55	```
56
57	## Core Capabilities
58
59	### 1. Alignment File Operations (SAM/BAM/CRAM)
60
61	Use the `AlignmentFile` class to work with aligned sequencing reads. This is appropriate for analyzing mapping results, calculating coverage, extracting reads, or quality control.
62
63	Common operations:
64	- Open and read BAM/SAM/CRAM files
65	- Fetch reads from specific genomic regions
66	- Filter reads by mapping quality, flags, or other criteria
67	- Write filtered or modified alignments
68	- Calculate coverage statistics
69	- Perform pileup analysis (base-by-base coverage)
70	- Access read sequences, quality scores, and alignment information
71
72	Reference: See `references/alignment_files.md` for detailed documentation on:
73	- Opening and reading alignment files
74	- AlignedSegment attributes and methods
75	- Region-based fetching with `fetch()`
76	- Pileup analysis for coverage
77	- Writing and creating BAM files
78	- Coordinate systems and indexing
79	- Performance optimization tips
80
81	### 2. Variant File Operations (VCF/BCF)
82
83	Use the `VariantFile` class to work with genetic variants from variant calling pipelines. This is appropriate for variant analysis, filtering, annotation, or population genetics.
84
85	Common operations:
86	- Read and write VCF/BCF files
87	- Query variants in specific regions
88	- Access variant information (position, alleles, quality)
89	- Extract genotype data for samples
90	- Filter variants by quality, allele frequency, or other criteria
91	- Annotate variants with additional information
92	- Subset samples or regions
93
94	Reference: See `references/variant_files.md` for detailed documentation on:
95	- Opening and reading variant files
96	- VariantRecord attributes and methods
97	- Accessing INFO and FORMAT fields
98	- Working with genotypes and samples
99	- Creating and writing VCF files
100	- Filtering and subsetting variants
101	- Multi-sample VCF operations
102
103	### 3. Sequence File Operations (FASTA/FASTQ)
104
105	Use `FastaFile` for random access to reference sequences and `FastxFile` for reading raw sequencing data. This is appropriate for extracting gene sequences, validating variants against reference, or processing raw reads.
106
107	Common operations:
108	- Query reference sequences by genomic coordinates
109	- Extract sequences for genes or regions of interest
110	- Read FASTQ files with quality scores
111	- Validate variant reference alleles
112	- Calculate sequence statistics
113	- Filter reads by quality or length
114	- Convert between FASTA and FASTQ formats
115
116	Reference: See `references/sequence_files.md` for detailed documentation on:
117	- FASTA file access and indexing
118	- Extracting sequences by region
119	- Handling reverse complement for genes
120	- Reading FASTQ files sequentially
121	- Quality score conversion and filtering
122	- Working with tabix-indexed files (BED, GTF, GFF)
123	- Common sequence processing patterns
124
125	### 4. Integrated Bioinformatics Workflows
126
127	Pysam excels at integrating multiple file types for comprehensive genomic analyses. Common workflows combine alignment files, variant files, and reference sequences.
128
129	Common workflows:
130	- Calculate coverage statistics for specific regions
131	- Validate variants against aligned reads
132	- Annotate variants with coverage information
133	- Extract sequences around variant positions
134	- Filter alignments or variants based on multiple crit

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pysam

698stars61forks

View on GitHub

How to install pysam?

leonchaox/qinyan-academic-skills/pysam

$npx -y skills add LeonChaoX/qinyan-academic-skills --skill pysam

Installs into the current project.

Summary

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Files · 1

View on GitHub

SKILL.md

1	# Pysam
2
3	## Overview
4
5	Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.
6
7	## When to Use This Skill
8
9	This skill should be used when:
10	- Working with sequencing alignment files (BAM/CRAM)
11	- Analyzing genetic variants (VCF/BCF)
12	- Extracting reference sequences or gene regions
13	- Processing raw sequencing data (FASTQ)
14	- Calculating coverage or read depth
15	- Implementing bioinformatics analysis pipelines
16	- Quality control of sequencing data
17	- Variant calling and annotation workflows
18
19	## Quick Start
20
21	### Installation
22	```bash
23	uv pip install pysam
24	```
25
26	### Basic Examples
27
28	Read alignment file:
29	```python
30	import pysam
31
32	# Open BAM file and fetch reads in region
33	samfile = pysam.AlignmentFile("example.bam", "rb")
34	for read in samfile.fetch("chr1", 1000, 2000):
35	print(f"{read.query_name}: {read.reference_start}")
36	samfile.close()
37	```
38
39	Read variant file:
40	```python
41	# Open VCF file and iterate variants
42	vcf = pysam.VariantFile("variants.vcf")
43	for variant in vcf:
44	print(f"{variant.chrom}:{variant.pos} {variant.ref}>{variant.alts}")
45	vcf.close()
46	```
47
48	Query reference sequence:
49	```python
50	# Open FASTA and extract sequence
51	fasta = pysam.FastaFile("reference.fasta")
52	sequence = fasta.fetch("chr1", 1000, 2000)
53	print(sequence)
54	fasta.close()
55	```
56
57	## Core Capabilities
58
59	### 1. Alignment File Operations (SAM/BAM/CRAM)
60
61	Use the `AlignmentFile` class to work with aligned sequencing reads. This is appropriate for analyzing mapping results, calculating coverage, extracting reads, or quality control.
62
63	Common operations:
64	- Open and read BAM/SAM/CRAM files
65	- Fetch reads from specific genomic regions
66	- Filter reads by mapping quality, flags, or other criteria
67	- Write filtered or modified alignments
68	- Calculate coverage statistics
69	- Perform pileup analysis (base-by-base coverage)
70	- Access read sequences, quality scores, and alignment information
71
72	Reference: See `references/alignment_files.md` for detailed documentation on:
73	- Opening and reading alignment files
74	- AlignedSegment attributes and methods
75	- Region-based fetching with `fetch()`
76	- Pileup analysis for coverage
77	- Writing and creating BAM files
78	- Coordinate systems and indexing
79	- Performance optimization tips
80
81	### 2. Variant File Operations (VCF/BCF)
82
83	Use the `VariantFile` class to work with genetic variants from variant calling pipelines. This is appropriate for variant analysis, filtering, annotation, or population genetics.
84
85	Common operations:
86	- Read and write VCF/BCF files
87	- Query variants in specific regions
88	- Access variant information (position, alleles, quality)
89	- Extract genotype data for samples
90	- Filter variants by quality, allele frequency, or other criteria
91	- Annotate variants with additional information
92	- Subset samples or regions
93
94	Reference: See `references/variant_files.md` for detailed documentation on:
95	- Opening and reading variant files
96	- VariantRecord attributes and methods
97	- Accessing INFO and FORMAT fields
98	- Working with genotypes and samples
99	- Creating and writing VCF files
100	- Filtering and subsetting variants
101	- Multi-sample VCF operations
102
103	### 3. Sequence File Operations (FASTA/FASTQ)
104
105	Use `FastaFile` for random access to reference sequences and `FastxFile` for reading raw sequencing data. This is appropriate for extracting gene sequences, validating variants against reference, or processing raw reads.
106
107	Common operations:
108	- Query reference sequences by genomic coordinates
109	- Extract sequences for genes or regions of interest
110	- Read FASTQ files with quality scores
111	- Validate variant reference alleles
112	- Calculate sequence statistics
113	- Filter reads by quality or length
114	- Convert between FASTA and FASTQ formats
115
116	Reference: See `references/sequence_files.md` for detailed documentation on:
117	- FASTA file access and indexing
118	- Extracting sequences by region
119	- Handling reverse complement for genes
120	- Reading FASTQ files sequentially
121	- Quality score conversion and filtering
122	- Working with tabix-indexed files (BED, GTF, GFF)
123	- Common sequence processing patterns
124
125	### 4. Integrated Bioinformatics Workflows
126
127	Pysam excels at integrating multiple file types for comprehensive genomic analyses. Common workflows combine alignment files, variant files, and reference sequences.
128
129	Common workflows:
130	- Calculate coverage statistics for specific regions
131	- Validate variants against aligned reads
132	- Annotate variants with coverage information
133	- Extract sequences around variant positions
134	- Filter alignments or variants based on multiple crit

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6 picks

Type