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#+title: percent nucleotide identity threshold (pnit?)
* input
csv file, first row and first column are names, every other item is
the % identity of the names corresponding to the current cell.
#+name: input-table-example
| | seq1 | seq2 | seq3 |
| seq1 | | | |
| seq2 | 0.9 | | |
| seq3 | 0.32 | 0.11 | |
this shows ~seq2~ is 90% identical to ~seq1~, and ~seq3~ is 32% and 11%
identical to ~seq1~ and ~seq2~, respectively.
the csv file would look like this:
#+name: input-csv-example
#+begin_src text
,seq1,seq2,seq3
seq1,,,
seq2,0.9,,
seq3,0.32,0.11,
#+end_src
* output
csv file, two column, representing a pair where the value is at least
as large a given threshold.
given [[input-table-example][the example input table]], at a threshold of 32%, we should get:
#+name: output-table-example-32
| seq2 | seq1 |
| seq3 | seq1 |
or, in csv:
#+name: output-csv-example
#+begin_src text
seq2,seq1
seq3,seq1
#+end_src
* runners
#+name: process
#+begin_src shell :results file :file paplcv-nov-16-2024-aligned_mat-90.5.csv :var threshold=90.5 filename="inputs/PapLCV-Nov-16-2024-Aligned_mat.csv"
nix-shell --run "./pairwise.pl $threshold $filename"
#+end_src
#+RESULTS: process
[[file:paplcv-nov-16-2024-aligned_mat-90.5.csv]]
#+call: process[:file n-402-90.5.csv](threshold=90.5, filename="n-402.csv")
#+RESULTS:
[[file:n-402-90.5.csv]]
#+call: process[:file n-402-93.5.csv](threshold=93.5, filename="n-402.csv")
#+RESULTS:
[[file:n-402-93.5.csv]]
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