Forum:Sequence Finder Project - I want to hear from you

Question

[jonathan.earl.patterson]

Sequence Finder

I wrote a program that can be used to find specific nucleotide or peptide sequences from a FASTA file called Sequence Finder. This program currently a bit messy, but is available on my GitHub under the MIT License (basically free and free to do whatever you want with it). This application is meant to save you the time of having to write your own regex parsing expressions. It is written in python 3.

Why

Before I fully package this application, I would love to hear from members of this community about common tasks you have when analyzing sequences. Sequence Finder came from me throwing together a quick script for a friend, and then realizing it might save people time to not have to write scripts just to look for a few simple sequences. So my research into the topic was minimal, and my personal experience working with sequences was quite limited in my former molecular biology lab. Fast forward a few years and now I am a full stack developer who would love to contribute free tools to make your life easier. I would love to hear common pain points, and would be more than happy to credit anyone who suggests features on the GitHub repository and on the main website (not launched yet).

Thanks for your time and for any suggestions you have. Also if you do need a really specific script for a niche problem feel free to post that as well as I am happy to write little scripts whenever I can.

Best,
Jonathan

[GenoMax]

to find specific nucleotide or peptide sequences from a FASTA file

Can you include a preview of how your tool works/is different than other tools out there? There are no examples/information in this post or on the main GitHub page for Sequence_Finder to entice me to give this a second look.

[jonathan.earl.patterson]

Thanks for the suggestion genomax. I will definitely be getting a preview and tutorials up for how to use the program within the next day or two. I am quite unfamiliar with the current software landscape, but I realize it is hard to get a snapshot of similar tools without a thorough description of my own tool. Thanks again!

[Ram]

meant to save you the time of having to write your own regex parsing expressions

Is there another way I can convey the pattern I'm thinking of to a tool to fetch sequences matching that pattern than, say, the closest plain text-pattern matching algorithm that exists right now? Unless a tool somehow can read my mind flawlessly, I daresay a regex is the closest anything can get to me conveying what I want in the most succinct manner possible.

[jonathan.earl.patterson]

I completely agree with you Ram if you are experienced with regex syntax and know how to apply that already. As genomax suggested, I should've posted something about what the program does and how it works on my GitHub before posting here. I'll edit my post once I get a clear and concise description of the tool written up and posted on GitHub. Also I appreciate the skepticism as it may very well only be useful for my friend (entirely possible as I did not look into the market before writing the application). Thanks for your input!

[Ram]

Disclaimer: I'm a regex maniac (grep -E defaulter that's trying to move on to grep -P mastery), hence my comment on regular expressions. If your tool helps beginners, that's great, but IMO grep with a UI already exists in tools such as notepad++/BBEdit/TextWrangler/Sublime.

I look forward to reading your tool description!