Fast way to extract hg19 sequences with Biopython?
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Creating BLASTN database for viruses
written by emiliomastriani •
-
Extracting CDS using python
written by Davi.marcon •
-
Extract sequences from the raw reads
written by Jusnib •
-
Fasta file display and edition
written by M.Nadeem Khan •
-
Is there a way to fetch genomic sequences at given coordinates without downloading fasta files?
written by ericbrenner •
-
Popen Blat has different behavior than same syntax in shell
written by nchuang
-
Using a Multiple Seq Alignment tool for pairwise alignments possible?
written by nchuang
-
Tool: Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
written by Matt Shirley
-
Tests For Neutrality On Large Datasets?
written by Dj1 •
-
Blastx Against Swissprot
written by User 1330 •
You could use
samtools faidxin the meantime: Getting Sequence Based On Chromosome No And Coordinates From Whole Genome Fasta Filewow that looks so simple. I will try to subprocess it. Thanks!
Try
pip install --user pyfaidx. Then you should have thefaidxscript in$HOME/.local/bin.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.