菜单
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
| name | sam-bam-basics |
| description | View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure. |
| tool_type | cli |
| primary_tool | samtools |
Reference examples tested with: pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
pip show <package> then help(module.function) to check signatures<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Read a BAM file" → Open a binary alignment file and iterate over aligned reads with their mapping coordinates, flags, and quality scores.
pysam.AlignmentFile() (pysam)samtools view (samtools)scanBam() (Rsamtools)View and convert alignment files using samtools and pysam.
| Format | Description | Use Case |
|---|---|---|
| SAM | Text format, human-readable | Debugging, small files |
| BAM | Binary compressed SAM | Standard storage format |
| CRAM | Reference-based compression | Long-term archival, smaller than BAM |
@HD VN:1.6 SO:coordinate
@SQ SN:chr1 LN:248956422
@RG ID:sample1 SM:sample1
@PG ID:bwa PN:bwa VN:0.7.17
read1 0 chr1 100 60 50M * 0 0 ACGT... FFFF... NM:i:0
Header lines start with @:
@HD - Header metadata (version, sort order)@SQ - Reference sequence dictionary@RG - Read group information@PG - Program used to create fileAlignment fields (tab-separated):
samtools view input.bam | head
samtools view -h input.bam | head -100
samtools view -H input.bam
samtools view input.bam chr1:1000-2000
samtools view -c input.bam
Goal: Convert between SAM (text), BAM (binary), and CRAM (reference-compressed) alignment formats.
Approach: Use samtools view with format flags (-b for BAM, -C for CRAM, -h for SAM with header). CRAM requires a reference FASTA with -T.
samtools view -h -o output.sam input.bam
samtools view -b -o output.bam input.sam
samtools view -C -T reference.fa -o output.cram input.bam
samtools view -b -T reference.fa -o output.bam input.cram
samtools view -b input.sam > output.bam
| Flag | Decimal | Meaning |
|---|---|---|
| 0x1 | 1 | Paired |
| 0x2 | 2 | Proper pair |
| 0x4 | 4 | Unmapped |
| 0x8 | 8 | Mate unmapped |
| 0x10 | 16 | Reverse strand |
| 0x20 | 32 | Mate reverse strand |
| 0x40 | 64 | First in pair |
| 0x80 | 128 | Second in pair |
| 0x100 | 256 | Secondary alignment |
| 0x200 | 512 | Failed QC |
| 0x400 | 1024 | PCR duplicate |
| 0x800 | 2048 | Supplementary |
samtools flags 147
# 0x93 147 PAIRED,PROPER_PAIR,REVERSE,READ2
| Op | Description |
|---|---|
| M | Alignment match (can be mismatch) |
| I | Insertion to reference |
| D | Deletion from reference |
| N | Skipped region (introns in RNA-seq) |
| S | Soft clipping |
| H | Hard clipping |
| = | Sequence match |
| X | Sequence mismatch |
Example: 50M2I30M = 50 bases match, 2 base insertion, 30 bases match
Goal: Read and manipulate alignment data programmatically in Python.
Approach: Use pysam.AlignmentFile to open BAM/CRAM files, iterate over reads, and access properties like coordinates, flags, CIGAR, and tags.
import pysam
with pysam.AlignmentFile('input.bam', 'rb') as bam:
for read in bam:
print(f'{read.query_name}\t{read.reference_name}:{read.reference_start}')
with pysam.AlignmentFile('input.bam', 'rb') as bam:
for sq in bam.header['SQ']:
print(f'{sq["SN"]}: {sq["LN"]} bp')
with pysam.AlignmentFile('input.bam', 'rb') as bam:
for read in bam:
print(f'Name: {read.query_name}')
print(f'Flag: {read.flag}')
print(f'Chrom: {read.reference_name}')
print(f'Pos: {read.reference_start}') # 0-based
print(f'MAPQ: {read.mapping_quality}')
print(f'CIGAR: {read.cigarstring}')
print(f'Seq: {read.query_sequence}')
print(f'Qual: {read.query_qualities}')
break
with pysam.AlignmentFile('input.bam', 'rb') as bam:
for read in bam:
if read.is_paired and read.is_proper_pair:
if read.is_reverse:
strand = '-'
else:
strand = '+'
print(f'{read.query_name} on {strand} strand')
with pysam.AlignmentFile('input.bam', 'rb') as bam:
for read in bam.fetch('chr1', 1000, 2000):
print(read.query_name)
with pysam.AlignmentFile('input.bam', 'rb') as infile:
with pysam.AlignmentFile('output.sam', 'w', header=infile.header) as outfile:
for read in infile:
outfile.write(read)
with pysam.AlignmentFile('input.bam', 'rb') as infile:
with pysam.AlignmentFile('output.cram', 'wc', reference_filename='reference.fa', header=infile.header) as outfile:
for read in infile:
outfile.write(read)
| Task | samtools | pysam |
|---|---|---|
| View BAM | samtools view file.bam | AlignmentFile('file.bam', 'rb') |
| View header | samtools view -H file.bam | bam.header |
| Count reads | samtools view -c file.bam | sum(1 for _ in bam) |
| Get region | samtools view file.bam chr1:1-1000 | bam.fetch('chr1', 0, 1000) |
| BAM to SAM | samtools view -h -o out.sam in.bam | Open with 'w' mode |
| SAM to BAM | samtools view -b -o out.bam in.sam | Open with 'wb' mode |
| BAM to CRAM | samtools view -C -T ref.fa -o out.cram in.bam | Open with 'wc' mode |