Fast way to extract hg19 sequences with Biopython?

Question

[nchuang]

I am trying to extract a list of 5kb sequences from hg19 genome. However it takes a very long time to Bio.SeqIO.parse() all of the genome into memory, and even using Bio.SeqIO.index() also takes a long time as well.

What is a fast way to do this or this is a limitation of python?

I'm waiting for my admin to install pyfaidx for me and I will see how that one does too.

[GenoMax]

You could use samtools faidx in the meantime: Getting Sequence Based On Chromosome No And Coordinates From Whole Genome Fasta File

[nchuang]

wow that looks so simple. I will try to subprocess it. Thanks!

[Matt Shirley]

Try pip install --user pyfaidx. Then you should have the faidx script in $HOME/.local/bin.

[nchuang]

I don't have root and pip is not even installed on the default version 2.4. They did install 3.4 for me but I had to add it to path. I don't think I have pip for that install either.