how to extract the gene sequence according to its coordinates on the reference genome?

Question

[zhangdengwei]

hi, how to extract the gene sequence according to its coordinates on the reference genome? Thanks!

[Joe]

What have you tried? I would suggest using BioPython and string slicing notation of which there are many examples on the forum.

You also haven’t told us what format your data is in.

[lieven.sterck]

this is a very briefly formulated question ! perhaps read this first : How To Ask Good Questions On Technical And Scientific Forums

What kind of input files do you have? do you want to do this for a single gene, multiple genes, all genes ... ? Do take the effort to include a bit more info to get more suitable answers.

[Emily]

And do you want the whole gene (introns and exons), cDNA, CDS, protein sequences?

[zhangdengwei]

I am sorry I don't state my question clearly. I am writing a python script to integrate my pipeline, and there is a step which I need to get the DNA sequence by a random pair of start and end position from a quite large FASTA file. So what I want to ask is just which tool or approach can handle it quickly, biopython or else?

[lieven.sterck]

if it's within a python pipeline / project, then yes likely biopython is the more sensible option. Otherwise you could for instance also get this through blast if you have a blastdb formatted version of your fasta file

[Joe]

Take a look at my code here https://github.com/jrjhealey/bioinfo-tools/blob/master/Genbank_slicer.py

The same approach would work for fasta files as well as Genbanks etc.

[zhangdengwei]

Thank you very much for your time!

Answer 1

[zhangdengwei]

I found a python module named "pyfaidx" which could satisfy my needs. It can make things simple which fetch sequence from a FASTA file. And here is the link https://pypi.org/project/pyfaidx/#description

[Assa Yeroslaviz]

if you're done with it, close it