Read A .Bam File With Biopython Module Bgzf Without Samtools

Question

[loic.laureote]

hi, I tried to read a .bam file, by uncompress the file with bgzf module provided by biopython but only some indexed parts are readable. I saw that the file is build by different compressed block, but how to read it with biopython ?

from Bio import SeqIO
import gzip
from Bio import bgzf
import struct
import gzip
handle = bgzf.BgzfReader("Example.bam", "r")
print handle.read(100)

Thanks for your help !!

[matted]

Why not use pysam?

[loic.laureote]

pysam is a python wrapper of samtools

[matted]

Sure, but I guess I meant to ask if there's a specific reason you don't want to use samtools (even if wrapped in python).

[loic.laureote]

there is not easy way to install it on windows.

Answer 1

[Peter]

The current versions of Biopython do NOT include a SAM/BAM parser, just the BGZF code which handles random access to the compressed file, see: http://blastedbio.blogspot.co.uk/2011/11/bgzf-blocked-bigger-better-gzip.html

(And as noted above, try pysam https://code.google.com/p/pysam/ for a Python SAM/BAM library wrapping the samtools C API)