SAM Format

Stream SAM (Sequence Alignment/Map) text alignments as one record per read.

Overview

Property	Value
Format id	sam
Class	SAMIterable
Extensions	.sam
Read	Yes
Write	No
Extra	alignment (pysam)
Maturity	stable

Record shape

Same fields as BAM:

{
    "query_name": "read1",
    "flag": 0,
    "reference_id": 0,
    "reference_start": 100,
    "mapping_quality": 60,
    "cigarstring": "50M",
    "next_reference_id": -1,
    "next_reference_start": -1,
    "template_length": 0,
    "query_sequence": "ACGT...",
    "query_qualities": "IIII...",
}

Requires a filename (streams not supported).

Usage

from iterable import open_iterable

with open_iterable("alignments.sam", format="sam") as source:
    for aln in source:
        print(aln["query_name"], aln["reference_start"])

Install with pip install iterabledata[alignment].

See also

• BAM — binary alignments
• Supported formats