I needed to have a simple FASTA file parser without using Biopython. There are just cases when you need to use some functions in Biopython but you can't install the whole package. In my case,  I wanted to handle and process sequences in FASTA format within a Google App Engine web app where it is not possible to install Python packages that have C extensions. Some of you may have other use cases, like when you want just the SeqIO.index() function to parse FASTA files. This is exactly what this short script tries to mimic. It has most of the methods and attributes of an indexed FASTA file using Bio.SeqIO in Biopython.

One of the routines in bioinformatics is fetching the sequence of a protein or DNA of a given accession number into either FASTA or Genbank format. I ran into the need of creating a short script that can do this for me and this is what I'm sharing here. It depends on modules from the Biopython package.

Whenever I need to accomplish something when I am programming, I first turn to Google to search if someone else already did something similar. Sometimes I am lucky to find complete working codes but sometimes I need to modify a bit. In either case, these are time-savers.  This is the motivation for my snippets post series. In simple terms, snippets are short re-usable codes.

We were born with an ability to think. This seems to be an evolutionary adaptation and a very powerful one. By our power to think, we have the power to have greater influence on our surroundings and that translates to greater chance of survival. Our mind is built with a sense of orderliness but at the same time we have a built-in sense that we can reorder things for our benefits. 

I am beginning to think that the study of natural systems is a desperate attempt of the poor and limited human mind to grasp the laws and mechanisms of nature. Investigations in natural science can only proceed by assuming that certain limitations don't really matter so much or by assuming that they are addressed well.