Entire Sequence from Bam File using Python Pysam Module

Question

[BioICoder]

Hello there,

Is there away to be able to extract the entire chromosome sequence from the bam file using the Pysam Python module? I am trying to analyze the entire aligned sequence of some chromosome for instance chr1 from NGS.

Thanks a lot in advance.

[Medhat]

if you mean extracting the reads aligned to chr1 you can use

import pysam
samfile = pysam.AlignmentFile("your.bam", "rb")
for read in samfile.fetch('chr1', chr_beginning, chr_end):
          print read
samfile.close()

and if you want extract your chromosome in bam format using samtools

samtools index your.bam
samtools view -bh your.bam chr1  > small.bam