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  • 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 find-reciprocal.py which is can be found here

    https://bitbucket.org/ctb/ngs-course...-reciprocal.py

    this script need two other models, which can be found here
    https://bitbucket.org/ctb/ngs-course/src/tip/blast/

    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
    cheers,
    Last edited by nicedad; 06-07-2012, 06:28 AM. Reason: forgot something

  • #2
    Have you checked the .csv files to confirm that they look ok (have the expected format)?

    Comment


    • #3
      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.

      Fabio

      Comment

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