Bam file to Consensus Fasta/fastq in python

[daniel_navarro]

Hello!

Summary:
I want to get the same result as I get from this command, but in python (BioPython/Pysam):

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

Full story:
I need to extract the consensus fasta from an aligned bam file, currently I'm doing it with samtools, but I'll be more than happy if I can implement it in python without 3rd party tools. That's important because this step is an intermediate step, so I need this fasta sequence to play with it.

Thanks everyone for your help.

Best,

Daniel.

[rnaeye]

Can't you call these tools within your Python script? As long as machine you are running have the tools installed, it should be fine.

Editing:
Sorry, when read you message a second time, I realized that you said you do not want to use third party tools.