[Seqinr-commits] r2055 - pkg/inst/sequences

[noreply at r-forge.r-project.org]

Author: jeanlobry
Date: 2017-07-04 13:30:32 +0200 (Tue, 04 Jul 2017)
New Revision: 2055

Added:
   pkg/inst/sequences/kaks-torture.fasta
Log:
new test file for kaks

Added: pkg/inst/sequences/kaks-torture.fasta
===================================================================
--- pkg/inst/sequences/kaks-torture.fasta	                        (rev 0)
+++ pkg/inst/sequences/kaks-torture.fasta	2017-07-04 11:30:32 UTC (rev 2055)
@@ -0,0 +1,145 @@
+;
+; This is a test file for the kaks() function from seqinr package.
+; This is an alignment of the 64 possible codons so that kaks
+; values are computed for possible pairs of one-codon sequences.
+;
+; Only finite values should be returned. Expected values are given
+; in data(kaks-torture).
+;
+; This file was generated with the following R script :
+;
+; x <- words() # The 64 codons
+; aa1 <- sapply(x, function(x) translate(s2c(x)))
+; aa3 <- aaa(aa1)
+; names <- paste(x, aa1, aa3, sep = "-")
+; sequences <- as.list(toupper(x))
+; write.fasta(sequences, names, file.out = "kaks-torture.fasta")
+; 
+>aaa-K-Lys
+AAA
+>aac-N-Asn
+AAC
+>aag-K-Lys
+AAG
+>aat-N-Asn
+AAT
+>aca-T-Thr
+ACA
+>acc-T-Thr
+ACC
+>acg-T-Thr
+ACG
+>act-T-Thr
+ACT
+>aga-R-Arg
+AGA
+>agc-S-Ser
+AGC
+>agg-R-Arg
+AGG
+>agt-S-Ser
+AGT
+>ata-I-Ile
+ATA
+>atc-I-Ile
+ATC
+>atg-M-Met
+ATG
+>att-I-Ile
+ATT
+>caa-Q-Gln
+CAA
+>cac-H-His
+CAC
+>cag-Q-Gln
+CAG
+>cat-H-His
+CAT
+>cca-P-Pro
+CCA
+>ccc-P-Pro
+CCC
+>ccg-P-Pro
+CCG
+>cct-P-Pro
+CCT
+>cga-R-Arg
+CGA
+>cgc-R-Arg
+CGC
+>cgg-R-Arg
+CGG
+>cgt-R-Arg
+CGT
+>cta-L-Leu
+CTA
+>ctc-L-Leu
+CTC
+>ctg-L-Leu
+CTG
+>ctt-L-Leu
+CTT
+>gaa-E-Glu
+GAA
+>gac-D-Asp
+GAC
+>gag-E-Glu
+GAG
+>gat-D-Asp
+GAT
+>gca-A-Ala
+GCA
+>gcc-A-Ala
+GCC
+>gcg-A-Ala
+GCG
+>gct-A-Ala
+GCT
+>gga-G-Gly
+GGA
+>ggc-G-Gly
+GGC
+>ggg-G-Gly
+GGG
+>ggt-G-Gly
+GGT
+>gta-V-Val
+GTA
+>gtc-V-Val
+GTC
+>gtg-V-Val
+GTG
+>gtt-V-Val
+GTT
+>taa-*-Stp
+TAA
+>tac-Y-Tyr
+TAC
+>tag-*-Stp
+TAG
+>tat-Y-Tyr
+TAT
+>tca-S-Ser
+TCA
+>tcc-S-Ser
+TCC
+>tcg-S-Ser
+TCG
+>tct-S-Ser
+TCT
+>tga-*-Stp
+TGA
+>tgc-C-Cys
+TGC
+>tgg-W-Trp
+TGG
+>tgt-C-Cys
+TGT
+>tta-L-Leu
+TTA
+>ttc-F-Phe
+TTC
+>ttg-L-Leu
+TTG
+>ttt-F-Phe
+TTT