codon adaptation index (CAI) estimation
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5.3 years ago
rthapa ▴ 90

I am trying to get codon adaptation index score for all the fasta sequences. I have split the multifasta file to individual files with each fasta sequence. I tried to get CAI score using CAI python package and looping for each file. Although I could get scores result for some of my fasa files, after sometime it gave an error. It seems like one of my fasta file does not have fasta sequence divisible by 3. Is there any suggestion how could I deal with this? Thanks

Traceback (most recent call last):
  File "<stdin>", line 11, in <module>
  File "/usr/local/lib/python3.7/dist-packages/CAI/CAI.py", line 186, in CAI
    raise ValueError("Input sequence not divisible by three")
ValueError: Input sequence not divisible by three
codon-usage • 1.1k views
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Entering edit mode
23 days ago
Stefanie • 0

you could create an exception in your code to continue the program instead of halting at that file, skip that file, or open the file and iinvestigate above line 186 to determine if there is missing data. From my understanding, all coding. regions of protein total a number that is always divisible by 3. I realize this is a very old question and you probably figured out how to manage it by. now, but I thought I would answer it in case anyone else stumbles across this inquiry and wants to know.

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