Counting the number of occurrence of a particolar letter in a string iteratively with a moving window like process
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HI! I have this kind of problem:
STR='AAAQQQPPPTTTCCCPPAAANNNDDDAAATTPPPPNNNAAA'
%Random Amino acidic sequence
Having this kind of sequence I want to count the number of occurrences that I would find using a sliding window process.
Like I give you my window's length and slinding this i get for each iteration a new pattern of aa where i count a new number of a particular residue. In my particular problem I have a cellarray containing 5000 and more sequences so I would prefer to avoid a double for loop. Anyone knows some kind of function or itaration that can be usefull?
Thanks very much!
2 commentaires
Image Analyst
le 4 Déc 2018
Don't worry about a few thousand iterations - it will be very very fast.
So you want some kind of histogram (count) of the letters at each window location as the window slides along? So you'd have thousands of histograms?
Have you tried reshape() to shape it into a 2-D matrix and then sum across the matrix?
Réponses (2)
Bio_Ing_Sapienza
le 4 Déc 2018
1 commentaire
Image Analyst
le 4 Déc 2018
movmean() slides over by one element. reshape() will let you, in effect, move in "jumps" of the window size. How much do you want the window to slide over each time?
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