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| author | Brian Cully <bjc@spork.org> | 2025-10-14 12:29:55 -0400 |
|---|---|---|
| committer | Brian Cully <bjc@spork.org> | 2025-10-14 12:29:55 -0400 |
| commit | d1b7083081fd905cc351a83565885ee8ba13a0e1 (patch) | |
| tree | 929453058c916cf109fc52788aa4a164e12e92d1 /README.org | |
| parent | 95bb2e116201d877cf2cc0ff8e1c962cfc71731c (diff) | |
| download | pnit-d1b7083081fd905cc351a83565885ee8ba13a0e1.tar.gz pnit-d1b7083081fd905cc351a83565885ee8ba13a0e1.zip | |
Diffstat (limited to 'README.org')
| -rw-r--r-- | README.org | 10 |
1 files changed, 7 insertions, 3 deletions
@@ -1,6 +1,10 @@ #+title: percent nucleotide identity threshold (pnit?) -* input +* web code +run with ~make serve~. see ~shell.nix~ for requirements. + +* perl code +** input csv file, first row and first column are names, every other item is the % identity of the names corresponding to the current cell. @@ -22,7 +26,7 @@ the csv file would look like this: seq3,0.32,0.11, #+end_src -* output +** output csv file, two column, representing a pair where the value is at least as large a given threshold. @@ -38,7 +42,7 @@ or, in csv: seq3,seq1 #+end_src -* runners +** 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" |