https://divingintogeneticsandgenomics.com/tags/fasta/ Recent content in Fasta on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 24 Feb 2015 08:19:00 -0800 https://divingintogeneticsandgenomics.com/archive/fetch-genomic-sequences-from-coordinates/ Tue, 24 Feb 2015 08:19:00 -0800 https://divingintogeneticsandgenomics.com/archive/fetch-genomic-sequences-from-coordinates/ One of the most common tasks in bioinformatics is to retrieve DNA sequences according to the given coordinates (in bed format or others). I had a post previously to describe this, and if you google around, you will find many other methods. I am going to compile all the methods that I found in this post. Please refer to the posts in biostar: https://www.biostars.org/p/19267/ https://www.biostars.org/p/3137/ https://www.biostars.org/p/56/ Method 1: Using DAS server https://divingintogeneticsandgenomics.com/archive/use-python-to-change-the-header-of-a-fasta-file-based-on-a-dictionary-in/ Tue, 22 Jul 2014 12:37:00 -0700 https://divingintogeneticsandgenomics.com/archive/use-python-to-change-the-header-of-a-fasta-file-based-on-a-dictionary-in/ I saw on SEQanwser, someone asked this question here, and I used python to resolve this problem. I have not written in python for so long, I've been using R for a long time. This provide me a good practice opportunity. The basic problem is to format some files, and I know it can be done by other tools like sed and awk ( see an awk solution below), but python just gives you much more flexibility in terms of what you can do and gives you more readability.