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Convert fasta into a Numeric Summarization Vector (NSV) #1895

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solshiferaw opened this issue Sep 26, 2019 · 2 comments
Open

Convert fasta into a Numeric Summarization Vector (NSV) #1895

solshiferaw opened this issue Sep 26, 2019 · 2 comments

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@solshiferaw
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solshiferaw commented Sep 26, 2019 •
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I want to convert fasta file to NSV for k-mers frequency count. What code need to written in python and how to load file? Thank you!
@standage
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Hi Solshi!

Could you please describe with a bit more detail what the contents of the NSV will be and what sequence characteristics they will summarize? An example of what you expect this vector to look like would help as well.

@solshiferaw solshiferaw mentioned this issue Sep 27, 2019
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@solshiferaw
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Dear!
My NSV file containing frequency of nuclietied, kmers
Suppose ...
Fasta file contain

RF00050|AECL01000049.1/43972-43822
GGUUGUUCUCAGGGCGGGGUGCAAUUCCCCACCGG
RF00050|CP000628.1/2430019-2430165
GACCGUUCUCAGGGCGGGGUGAGAUUCCCCAC
conver to kmer frequency count(a, aa, aaa,aaaaa, aaaaaa....) aa, au, cua, cug, ggg, aaac........
and convert those kmer frequency into vector to analyse in Weka.
Thank you!

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@standage @solshiferaw