Convert .fa FASTA file to Excel / Text Tab Delimited format

Just recently i was requested by my friend to help convert a text document to an Excel sheet which could be understood easily. Firstly i could not directly open the file in Notepad Or Excel as it was not properly supported.

Later when i forced it open in Notepad, it was just massive strings of text with nothing to interpret. I wanted to know what the file format is. So .fa file format is

FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985.[1] Its legacy is the FASTA format which is now ubiquitous in bioinformatics.     Source: Wikipedia

I had never encountered such file format and was excited to know something in DNA sequencing.

 

Google is the best tool to get the directions to a solution, i searched google with keywords to convert .fa file to excel. However I realised there was ni ready tool or technique to convert such file. Yes, you could manually edit each of 1500 lines and spend 2-3 hours to get it done without being sure of the accuracy.

 

While googling I stumbled upon a youtube video shows the same intended conversion in some Orange software. Initially i was not sure what software it is, but after switching to HD mode, i realised the software was Orange Canvas an open source data visualisation software, which you can download at http://orange.biolab.si/

 

 

These people had created a special widget to be added with orange canvas, It would convert the data from a fasta file to a usable, easily understood form in tabbed format.

 

Installing Orange was simple and I allowed whatever addon it asked for. Finally Orange setup was completed and the software was installed.

Following is  a screen shot how orange installation looks.



Later i Downloaded (Download from: https://github.com/1withforce/FileEngage) the GitHub Project and moved files as per instructions on Readme.md file which said:

File widget with universal converter compatibility (formerly OrangeFasta)
===========
V 1.0
===========

Orange file widget has built-in fasta converter.
Icon needs to go in ~/.../orange/OrangeWidgets/Data/icons/
converterClass needs to go in ~/.../orange/OrangeWidgets
OWFileEngage needs to go in ~/.../orange/OrangeWidgets/Data

 

Orange Canvas Home screen
Orange Canvas Home screen
Loading the File
Loading the File

How does this software work:

The white blank area which you see below the icons is the Canvas Area, similar to that of a painting canvas. The difference is only that you dont use water color Or brushes to paint :D. Just click on the desired icon and drag-drop it in the canvas.

  • First thing we need is: File
  • Next we need to Load the Data file (which can be Fasta Or Other format)
  • Double click on the File Icon and a Pop-up will appear where we can select the file source to load the data

 

At this moment, the File Engage Widget prepared by those 2 guys was not added. Once added, we get a new icon called File Engage

Icon

 

After installing FileEngage widget

 

Loaded the desired .fa file

 

Add the Data Table widget

 

Copy and Paste in Excel Or Notepad

Thats it, you are done.

One response to “Convert .fa FASTA file to Excel / Text Tab Delimited format”

  1. Hi. I’m trying to convert a bed file showing (chr number, start position and stop position) into fasta format for the mouse genome build mm9. The file is for several hundred examples. Is there an easy way these sequence can be extracted. Galaxy doesn’t seem to have a function that can do this.
    Thank you.

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.