SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Splitting FASTA files aw90 Bioinformatics 1 07-16-2013 04:28 AM
Combine two FASTA files Calico Bioinformatics 5 09-26-2012 12:35 PM
compare two Fasta files acyrocks Bioinformatics 7 09-26-2012 07:22 AM
Doubt about .abi files and .fasta files fc35802 Bioinformatics 2 02-28-2012 10:05 AM
454 fasta files jordi 454 Pyrosequencing 0 12-16-2010 04:32 AM

Reply
 
Thread Tools
Old 07-02-2014, 07:15 AM   #1
medinab
Junior Member
 
Location: Texas

Join Date: Jun 2014
Posts: 3
Default Analyzing fasta files: BioPython

Hello!!!

I have a file with a list of accession numbers for the organisms of my interest. I also have two other fast files, one with a list of large ribosomal subunits, and one with a list of small ribosomal subunits. What I am trying to do is to get both large and small ribosomal subunits for the organisms of my interest.

Basically, what I have to do is to compare three files and isolate duplicates in all three.

I was hoping you guys can help me figure out a script in BioPython that would help me get the information I want.

Thank you!!!
medinab is offline   Reply With Quote
Old 07-07-2014, 04:31 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

Create a set from the accession numbers, read the two fasta file and store the headers as a set. Now you can use intersection() method to get common elements.
https://docs.python.org/2/library/sets.html
TiborNagy is offline   Reply With Quote
Reply

Tags
biopython

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:08 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO