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Old 06-07-2012, 06:17 AM   #1
Location: Switzerland

Join Date: May 2011
Posts: 49
Default detect orthologs using reciprocal BLAST

Hi everyone,
I have to detect orthologs between two species using reciprocal BLAST, i.e. blasting the set A against the set B and then blasting the set B against the
set A. which means that am gona blast fasta file A aginst fasta file B (as the database or subject) and then blasting fasta ifle B agains fasta file A (as the database or subject).
The blast operation itself went properly with two .CVS files. my proplem now is to compair these two files that resulting from the tow blasting operations.
Thus one needs to use the above mentioned algorithm (reciprocal BLAST).

I used a python script called which is can be found here

this script need two other models, which can be found here

Unfortunately, I always get the following error form python interpreter:
error line 49 d1 = load_csv_to_dict(in_file_1) not known
error line 14 for (query_name, subject_name, score,expect) in csv.reader(open(filename)):

Seemingly, the .csv files have not been recognized!

hope there is a help in here

Last edited by nicedad; 06-07-2012 at 06:28 AM. Reason: forgot something
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Old 06-07-2012, 07:09 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091

Have you checked the .csv files to confirm that they look ok (have the expected format)?
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Old 06-07-2012, 07:37 AM   #3
The Snow
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Location: Italy

Join Date: Jun 2012
Posts: 7

I had a problem like this when I prepared the csv using Excel. Try to create it using Linux (e.g. gedit).

That was my case, I hope can work also for you.

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