How to open a BAM file in pysam?
The above command opens the file ex1.bam for reading. The b qualifier indicates that this is a BAM file. To open a SAM file, type: CRAM files are identified by a c qualifier: Reads are obtained through a call to the pysam.AlignmentFile.fetch () method which returns an iterator.
What do you need to know about pysam in Python?
Pysam is a python module that makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files. It is a lightweight wrapper of the htslib C-API. This page provides a quick introduction in using pysam followed by the API. See Working with BAM/CRAM/SAM-formatted files for more detailed usage instructions.
How to read and write SAM files in pysam?
import pysam samfile = pysam.AlignmentFile(“ex1.bam”, “rb”) Once a file is opened you can iterate over all of the read mapping to a specified region using fetch (). Each iteration returns a AlignedSegment object which represents a single read along with its fields and optional tags:
How to create a new bam file from scratch?
Each call to the iterator returns an object of the type pysam.PileupColumn that provides access to all the reads aligned to that particular reference position as well as some additional information: The following example shows how a new BAM file is constructed from scratch.
Is there a way to index BAM file by read name?
Simple methods, like using grep, are incredibly slow if you want to look for more than a few reads. Luckily, pysam allows you to index a bam file by read name (using pysam.IndexedReads (AlignmentFile)) while keeping the sort order.
How to open a SAM file in pysam?
To open a SAM file, type: import pysam samfile = pysam.AlignmentFile(“ex1.sam”, “r”) CRAM files are identified by a c qualifier: import pysam samfile = pysam.AlignmentFile(“ex1.cram”, “rc”)
How to create an alignment file in pysam?
f1 = pysam.AlignmentFile(‘ex1.bam’) f2 = pysam.AlignmentFile(‘ex1.sam’) template ( AlignmentFile) – when writing, copy header from file template. header ( dict or AlignmentHeader) – when writing, build header from a multi-level dictionary. The first level are the four types (‘HD’, ‘SQ’, …).