[CHNOSZ-commits] r557 - in pkg/CHNOSZ: . R demo inst inst/extdata inst/extdata/protein inst/extdata/thermo man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 13 04:30:57 CEST 2020
Author: jedick
Date: 2020-07-13 04:30:55 +0200 (Mon, 13 Jul 2020)
New Revision: 557
Added:
pkg/CHNOSZ/inst/extdata/protein/EF-Tu.aln
pkg/CHNOSZ/inst/extdata/protein/POLG.csv
pkg/CHNOSZ/inst/extdata/protein/rubisco.fasta
Removed:
pkg/CHNOSZ/demo/bison.R
pkg/CHNOSZ/inst/extdata/fasta/
pkg/CHNOSZ/inst/extdata/protein/DS11.csv
pkg/CHNOSZ/inst/extdata/protein/DS13.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/thermo/protein.csv
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/util.fasta.Rd
pkg/CHNOSZ/tests/testthat/test-add.protein.R
pkg/CHNOSZ/tests/testthat/test-affinity.R
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Remove DS11.csv and DS13.csv (now in JMDplots)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-13 02:30:55 UTC (rev 557)
@@ -1,6 +1,6 @@
-Date: 2020-07-12
+Date: 2020-07-13
Package: CHNOSZ
-Version: 1.3.6-30
+Version: 1.3.6-31
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/R/examples.R 2020-07-13 02:30:55 UTC (rev 557)
@@ -30,7 +30,7 @@
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
"ORP", "findit", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "wjd",
- "bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum", "bison",
+ "bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum",
"AkDi", "comproportionation"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/demo/00Index 2020-07-13 02:30:55 UTC (rev 557)
@@ -27,6 +27,5 @@
TCA Standard Gibbs energies of steps of the citric acid cycle
aluminum Reactions involving Al-bearing minerals
carboxylase Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase
-bison Average oxidation state of carbon in proteins for phyla at Bison Pool
AkDi Henry's constant of dissolved gases
comproportionation Gibbs energy of sulfur comproportionation
Deleted: pkg/CHNOSZ/demo/bison.R
===================================================================
--- pkg/CHNOSZ/demo/bison.R 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/demo/bison.R 2020-07-13 02:30:55 UTC (rev 557)
@@ -1,45 +0,0 @@
-# CHNOSZ/demo/bison.R
-# average oxidation state of carbon (ZC) of metagenome-derived
-# proteins in different microbial phyla at Bison Pool 20171217
-
-# set default xaxs, yaxs, and tcl here becuase they are affected by previous demos
-par(mar=c(3.5, 4, 2.5, 2), las=1, mgp=c(2.2, 0.8, 0), xaxs="r", yaxs="r", tcl=-0.5)
-# read the amino acid compositions
-aa.annot <- read.csv(system.file("extdata/protein/DS11.csv", package="CHNOSZ"), as.is=TRUE)
-aa.phyla <- read.csv(system.file("extdata/protein/DS13.csv", package="CHNOSZ"), as.is=TRUE)
-sites <- c("N", "S", "R", "Q", "P")
-sitenames <- paste("bison", sites, sep="")
-# the names of the phyla in alphabetical order (except Deinococcus-Thermus at end)
-phyla.abc <- sort(unique(aa.phyla$organism))[c(1:7,9:11,8)]
-# an abbreviation for Dein.-Thermus
-phyla.abbrv <- phyla.abc
-phyla.abbrv[[11]] <- "Dein.-Thermus"
-phyla.cols <- c("#f48ba5", "#f2692f", "#cfdd2a",
- "#962272", "#87c540", "#66c3a2", "#12a64a", "#f58656",
- "#ee3237", "#25b7d5", "#3953a4")
-# set Chlorobi color to NA because no line is needed (it's identifed only at one location)
-phyla.cols[4] <- NA
-# chemical formula and ZC of proteins
-pf.phyla <- protein.formula(aa.phyla)
-ZC.phyla <- ZC(pf.phyla)
-# set up plot
-plot(0, 0, xlim=c(1, 5), ylim=c(-0.23, -0.14), xlab="distance from source, m", ylab=NA, xaxt="n")
-distance <- c(0, 6, 11, 14, 22)
-axis(1, at=1:5, labels=distance)
-mtext(axis.label("ZC"), side=2, line=3, las=0)
-for(i in 1:length(phyla.abc)) {
- # skip Euryarchaeota because it occurs at one location, on top of Dein.-Thermus and Firmicutes
- if(phyla.abc[i]=="Euryarchaeota") next
- # which of the model proteins correspond to this phylum
- iphy <- which(aa.phyla$organism==phyla.abc[i])
- # the locations (of 1, 2, 3, 4, 5) where this phylum is found
- ilocs <- match(aa.phyla$protein[iphy], sitenames)
- # the plotting symbol: determined by alphabetical position of the phylum
- points(ilocs, ZC.phyla[iphy], pch=i-1, cex=1.2)
- # lines to connect the phyla
- lines(ilocs, ZC.phyla[iphy], type="c", col=phyla.cols[i], lwd=2)
-}
-text(c(4.75, 2.0, 4.0, 4.0, 4.0, 2.0, 3.0, NA, 2.9, 1.3, 3.0),
- c(-0.146, -0.224, -0.161, -0.184, -0.145, -0.201, -0.144, NA, -0.176, -0.158, -0.192),
- phyla.abbrv, cex=0.9)
-title(main="Bison Pool hot spring, Yellowstone National Park")
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-13 02:30:55 UTC (rev 557)
@@ -5,7 +5,7 @@
% macros
\newcommand{\H2O}{\ifelse{latex}{\eqn{\mathrm{H_{2}O}}}{\ifelse{html}{\out{H<sub>2</sub>O}}{H2O}}}
-\section{Changes in CHNOSZ version 1.3.6-28 (2020-07-10)}{
+\section{Changes in CHNOSZ version 1.3.6-31 (2020-07-13)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -77,7 +77,10 @@
\item Revise \samp{OBIGT.Rmd} to reduce the size of the HTML file and
make deep linking to individual sections work.
- \item Remove vignette \samp{hotspring.Rnw}.
+ \item Remove vignette \samp{hotspring.Rnw}, demo \samp{bison.R}, and
+ associated data files \samp{DS11.csv} and \samp{DS13.csv}. The plots are
+ now in the \samp{bison.Rmd} vignette in the \pkg{JMDplots} package
+ (\url{https://github.com/jedick/JMDplots}).
}
}
@@ -134,12 +137,14 @@
\item TODO: use https in refs.csv
- \item TODO: add hotspring.Rmd to JMDplots package.
-
\item TODO: move protein.equil() example (previously in equilibrium.Rnw) to JMDplots.
\item TODO: change add.obigt --> add.OBIGT on website (Fe-O-H-S example) when package is submitted to CRAN.
+ \item TODO: move extdata/bison to JMDplots package.
+
+ \item TODO: remove extdata/refseq (now in JMDplots).
+
}
}
Deleted: pkg/CHNOSZ/inst/extdata/protein/DS11.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/DS11.csv 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/inst/extdata/protein/DS11.csv 2020-07-13 02:30:55 UTC (rev 557)
@@ -1,106 +0,0 @@
-"protein","organism","ref","abbrv","chains","Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys","Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val","Trp","Tyr"
-"overall","bisonN","",40360,1,14.922,1.746,9.16,15.878,9.257,14.468,3.411,12.241,13.563,22.487,3.948,6.265,8.939,5.484,12.167,10.655,8.555,15.743,2.533,7.708
-"overall","bisonS","",50497,1,15.319,1.65,8.579,13.934,8.039,13.773,3.237,10.99,10.765,20.255,3.731,5.498,8.829,5.331,12.249,9.791,8.318,15.013,2.728,6.318
-"overall","bisonR","",43250,1,19.316,1.657,8.762,13.901,7.537,15.218,3.896,9.579,7.465,23.088,3.705,5.264,11.017,7.404,14.92,9.139,9.375,14.71,3.232,6.3
-"overall","bisonQ","",83790,1,19.892,1.985,9.262,11.632,7.118,14.472,4.135,10.287,6.095,21.305,3.849,5.547,10.512,8.425,14.349,9.991,10.214,14.059,3.13,5.544
-"overall","bisonP","",74082,1,19.797,1.918,9.114,11.631,6.978,14.24,4.033,10.121,5.911,21.131,3.832,5.454,10.365,8.079,14.349,9.612,10.002,14.098,3.117,5.619
-"transferase","bisonN","",2384,1,17.826,2.457,11.129,19.789,12.771,18.434,4.725,15.546,17.168,27.834,4.84,7.492,11.625,5.86,14.44,12.781,9.646,19.799,2.825,9.815
-"transferase","bisonS","",2593,1,17.772,2.041,10.087,16.539,10.111,16.445,4.142,13.171,12.829,23.834,4.344,6.18,10.771,5.235,14.137,10.99,8.821,17.86,2.766,7.589
-"transferase","bisonR","",2257,1,21.817,2.031,9.397,15.504,8.257,16.694,4.755,10.564,7.948,25.194,4.069,4.967,12.629,6.997,16.736,8.957,9.28,16.79,3.235,6.857
-"transferase","bisonQ","",4398,1,23.621,2.664,10.704,12.761,8.009,16.814,5.453,11.892,6.195,24.446,4.475,5.343,12.729,8.637,17.03,10.21,10.656,16.528,3.618,6.563
-"transferase","bisonP","",4136,1,23.071,2.522,10.406,12.653,7.816,16.052,5.253,11.748,6.214,23.646,4.378,5.349,12.33,8.165,16.673,9.798,10.279,16.348,3.5,6.567
-"transport","bisonN","",1285,1,19.84,1.037,8.664,13.107,12.286,18.088,2.977,14.872,11.693,30.72,5.205,6.607,10.183,6.345,11.893,13.233,10.914,19.511,2.919,8.018
-"transport","bisonS","",1731,1,20.432,1.014,8.227,12.449,10.46,17.786,2.848,14.377,9.782,28.434,5.119,5.841,9.946,6.023,12.526,12.376,10.652,19.434,2.961,6.861
-"transport","bisonR","",1591,1,24.206,1.109,8.411,12.995,10.58,19.485,3.503,12.388,7.338,32.636,4.95,5.469,11.757,7.957,15.659,10.889,11.277,19.404,3.561,6.64
-"transport","bisonQ","",3429,1,24.82,1.574,9.253,11.534,9.986,18.959,3.673,14.514,6.053,29.968,5.453,6.138,11.688,9.195,14.985,12.311,12.625,19.244,3.799,5.789
-"transport","bisonP","",2993,1,23.869,1.496,9.027,11.186,9.606,18.133,3.492,13.929,6.056,28.76,5.293,6.043,11.137,8.797,14.775,11.666,12.144,18.628,3.543,5.825
-"dehydrogenase","bisonN","",1258,1,20.49,2.546,12.002,18.99,9.459,20.089,4.488,14.651,15.539,23.797,5.347,7.723,11.893,5.762,13.851,11.467,10.343,20.96,2.909,8.579
-"dehydrogenase","bisonS","",1651,1,21.414,2.419,11.078,17.543,8.291,19.552,4.568,13.631,12.705,21.667,5.062,6.806,11.258,5.51,14.398,10.644,10.259,20.231,2.933,7.357
-"dehydrogenase","bisonR","",1604,1,25.935,2.426,10.322,17.398,7.773,20.044,5.481,12.022,8.829,24.266,5.012,5.994,13.442,7.458,16.666,9.518,11.405,19.183,3.057,7.135
-"dehydrogenase","bisonQ","",2626,1,26.278,2.805,10.937,14.164,7.284,19.232,5.445,12.777,7.498,22.39,5.125,6.38,12.343,8.323,15.813,10.537,11.936,18.081,2.956,6.329
-"dehydrogenase","bisonP","",2428,1,26.05,2.764,10.894,14.439,7.251,19.02,5.441,12.445,7.376,21.996,5.027,6.362,12.259,8.044,15.853,10.046,11.795,18.069,2.873,6.435
-"synthase","bisonN","",1509,1,18.371,2.543,11.486,20.482,10.113,18.758,4.72,14.913,16.131,25.031,4.993,7.036,10.965,5.895,14.054,11.603,9.995,20.034,2.43,8.892
-"synthase","bisonS","",1486,1,18.66,2.245,10.863,18.251,8.81,17.581,4.38,13.59,13.341,22.421,4.649,6.299,10.441,5.448,13.989,10.755,9.384,18.808,2.346,7.55
-"synthase","bisonR","",1206,1,23.016,2.061,10.303,17.033,7.735,18.004,5.31,11.715,8.744,24.674,4.641,5.219,12.451,7.054,16.362,9.416,10.366,17.314,2.48,6.867
-"synthase","bisonQ","",2323,1,24.109,2.678,11.151,14.443,7.532,17.814,5.737,12.635,7.205,23.575,4.784,5.874,12.35,9.04,16.23,10.512,11.628,16.704,2.759,6.558
-"synthase","bisonP","",2037,1,23.769,2.527,10.821,13.926,7.154,16.963,5.398,12.185,6.886,22.601,4.729,5.613,11.95,8.378,15.952,9.979,11.115,16.322,2.545,6.338
-"ATPase","bisonN","",1099,1,16.813,1.464,10.854,22.308,9.96,16.963,3.584,15.258,16.287,30.237,4.638,6.674,10.02,7.51,16.884,12.924,10.075,19.411,1.869,7.296
-"ATPase","bisonS","",1437,1,16.427,1.202,10.283,19.371,8.496,16.286,3.382,14.102,13.079,26.979,4.557,6.031,9.586,7.024,16.202,11.949,9.536,18.349,1.852,6.088
-"ATPase","bisonR","",1174,1,21.898,1.372,10.259,19.033,7.48,16.756,4.489,12.39,9.267,30.147,4.491,5.337,11.691,9.369,18.996,10.263,10.759,17.848,1.974,5.566
-"ATPase","bisonQ","",2235,1,22.826,1.753,11.458,16.338,7.383,16.647,4.888,13.645,7.743,28.441,5.008,6.03,11.391,11.146,18.409,11.835,12.236,17.421,2.128,5.078
-"ATPase","bisonP","",2038,1,22.99,1.694,11.194,16.487,7.119,16.254,4.872,13.245,7.558,28.283,4.924,5.828,11.048,10.811,18.672,11.174,11.879,17.581,2.009,5.152
-"kinase","bisonN","",677,1,16.511,1.818,10.617,18.4,9.625,17.768,3.871,13.498,14.539,25.739,4.168,6.26,8.846,5.529,14.093,11.572,8.861,18.31,1.852,6.882
-"kinase","bisonS","",836,1,18.638,1.821,10.422,16.734,8.283,17.706,3.78,12.522,11.354,23.611,4.12,5.683,9.295,5.562,14.764,11.002,9.315,17.92,2.169,5.589
-"kinase","bisonR","",819,1,24.486,1.764,10.426,17.683,7.592,18.879,4.972,11.294,7.768,28.418,4.343,5.125,12.371,8.369,18.432,9.884,10.906,17.79,2.773,5.543
-"kinase","bisonQ","",2040,1,25.404,2.379,12.046,15.717,7.421,18.296,5.591,13.392,6.95,27.756,4.741,6.24,12.689,11.192,18.016,12.251,12.713,17.947,2.768,5.503
-"kinase","bisonP","",1751,1,24.802,2.287,11.56,15.17,7.029,17.729,5.287,13.12,6.603,26.606,4.736,6.119,11.975,10.184,17.718,11.51,12.3,17.422,2.58,5.314
-"synthetase","bisonN","",1003,1,17.71,2.828,14.138,27.129,12.565,19.371,5.476,15.95,20.187,29.719,5.476,8.144,13.367,7.65,17.861,12.875,10.988,22.169,3.964,10.944
-"synthetase","bisonS","",1159,1,18.187,2.44,13.231,23.439,10.962,18.131,5.101,14.79,16.098,26.026,5.076,7.091,12.678,6.437,17.515,11.844,10.591,20.607,3.838,9.569
-"synthetase","bisonR","",891,1,22.727,2.574,12.952,22.348,10.497,18.761,5.941,13.478,12.154,28.167,5.228,6.772,15.007,9.015,19.727,10.164,11.758,18.761,3.981,9.429
-"synthetase","bisonQ","",1509,1,23.789,2.745,13.074,17.248,9.068,17.306,5.843,13.001,9.354,24.903,4.985,6.221,13.565,9.97,17.962,10.683,12.372,17.298,3.779,7.803
-"synthetase","bisonP","",1417,1,23.26,2.591,12.558,16.977,8.677,16.693,5.654,12.496,8.66,24.225,5.025,6.112,13.551,9.3,18.252,10.112,11.979,16.946,3.716,7.826
-"membrane","bisonN","",818,1,20.148,0.892,9.144,14.775,16.071,19.935,3.108,17.367,14.689,32.704,4.633,7.623,10.133,7.032,12.667,15.407,11.59,20.44,3.11,10.258
-"membrane","bisonS","",834,1,21.486,1.025,8.386,12.703,13.282,18.659,2.97,15.38,11.592,30.349,4.615,6.463,9.971,6.635,12.649,13.83,11.236,19.499,3.536,8.325
-"membrane","bisonR","",761,1,25.476,1.244,8.681,12.888,11.65,21.07,3.399,12.75,7.355,33.8,4.495,6.449,12.661,8.913,16.988,12.777,12.42,19.586,4.656,8.394
-"membrane","bisonQ","",1476,1,25.766,1.406,8.986,11.337,11.066,20.762,3.447,14.121,5.951,30.478,4.677,7.446,11.848,9.493,15.818,13.565,13.253,18.959,4.639,7.154
-"membrane","bisonP","",1305,1,25.992,1.349,8.741,10.794,10.684,20.141,3.458,13.569,5.726,30.691,4.731,6.804,11.668,8.904,15.9,13.017,13.036,19.05,4.746,7.251
-"permease","bisonN","",503,1,22.68,0.821,5.431,8.221,15.342,18.793,2.292,16.161,7.863,37.406,5.851,5.205,9.773,5.01,9.855,14.891,10.72,20.586,3.575,8.254
-"permease","bisonS","",748,1,23.842,0.822,5.341,7.723,13.509,19.119,2.31,15.983,6.215,34.941,5.928,4.862,9.765,5.053,10.658,13.749,11.215,20.584,3.77,7.566
-"permease","bisonR","",698,1,27.186,0.744,5.477,8.457,13.713,21.415,2.603,12.689,4.542,40.755,5.383,4.585,11.58,6.524,13.824,11.841,11.212,20.264,4.688,7.029
-"permease","bisonQ","",1568,1,26.457,1.239,6.206,7.508,12.466,20.071,2.57,16.172,3.781,35.101,5.985,5.13,11.049,7.531,13.226,12.999,12.55,20.295,5.073,5.96
-"permease","bisonP","",1369,1,25.953,1.272,5.938,7.226,12.197,19.419,2.506,15.758,3.751,34.306,5.959,5.154,10.633,7.143,13.053,12.316,12.066,20.11,4.627,5.995
-"hydrolase","bisonN","",558,1,15.842,2.172,10.697,17.595,9.084,15.803,5.828,12.461,13.468,23.165,4.296,6.272,10.061,5.242,13.043,9.975,8.668,16.918,2.618,7.763
-"hydrolase","bisonS","",684,1,17.148,2.124,10.975,16.136,8.883,15.718,5.7,11.997,11.254,21.924,4.3,5.844,10.224,5.291,13.674,9.838,8.782,16.635,2.982,6.798
-"hydrolase","bisonR","",632,1,21.331,1.962,10.419,15.812,7.782,16.6,6.272,10.253,7.551,23.709,4.149,5.245,12.642,6.91,16.212,9.114,9.418,15.426,3.435,6.845
-"hydrolase","bisonQ","",1271,1,22.437,2.541,11.737,13.408,7.784,16.308,6.747,11.338,6.266,22.988,4.5,5.597,12.578,8.581,16.017,10.11,11.027,15.505,3.596,6.773
-"hydrolase","bisonP","",1181,1,21.707,2.419,11.209,12.801,7.232,15.679,6.481,10.671,5.887,21.804,4.392,5.272,11.986,7.621,15.56,9.362,10.37,14.733,3.442,6.273
-"oxidoreductase","bisonN","",637,1,20.545,3.339,9.948,16.159,14.201,19.962,4.846,15.57,13.835,29.706,6.424,6.658,12.013,5.953,12.407,12.851,10.765,20.959,3.931,10.914
-"oxidoreductase","bisonS","",806,1,19.947,3.124,9.061,14.65,11.452,18.187,4.314,13.49,11.356,25.295,5.852,5.8,11.266,5.416,12.556,11.038,9.881,18.677,3.615,8.648
-"oxidoreductase","bisonR","",475,1,22.105,3.225,7.754,14.065,10.305,18.667,4.465,11.215,8.371,26.863,5.724,5.175,12.221,6.28,13.528,9.419,9.385,16.613,3.928,7.92
-"oxidoreductase","bisonQ","",1035,1,23.552,3.589,9.329,12.511,9.813,18.391,4.726,12.643,6.772,25.654,6.181,5.646,12.47,7.604,14.17,10.739,11.202,16.961,3.759,7.238
-"oxidoreductase","bisonP","",850,1,22.975,3.327,8.98,12.325,9.489,18.242,4.535,12.387,6.978,24.821,6.075,5.562,11.731,7.2,13.728,10.288,10.844,16.789,3.656,7.287
-"transcription","bisonN","",470,1,14.906,1.715,7.691,15.449,6.238,11.498,3.517,10.353,10.294,20.883,3.806,4.687,7.421,5.911,13.249,9.309,7.534,13.715,1.577,5.204
-"transcription","bisonS","",603,1,15.464,1.758,7.756,14.028,5.72,11.604,3.265,9.735,9.128,20.101,3.746,4.164,7.806,5.97,13.882,9.066,7.743,13.542,1.751,4.703
-"transcription","bisonR","",509,1,19.521,1.497,8.234,16.656,5.639,12.878,4.271,8.835,7.53,24.713,3.658,3.731,10.358,7.585,17.475,8.623,8.77,13.697,2.035,5.297
-"transcription","bisonQ","",1127,1,20.441,2.002,9.895,14.476,5.851,12.53,4.808,10.532,6.184,23.698,4.239,4.801,10.147,9.392,17.06,10.815,10.209,13.877,2.163,4.996
-"transcription","bisonP","",1038,1,20.119,1.922,9.512,14.456,5.677,12.502,4.765,10.48,6.075,23.203,4.24,4.793,10.063,9.13,17.133,10.284,10.011,13.978,2.158,5.06
-"peptidase","bisonN","",472,1,18.053,1.303,11.561,18.903,10.434,19.576,4.138,14.803,16.225,25.225,4.816,7.538,11.153,6.343,14.155,13.032,10.485,19.22,3.021,9.672
-"peptidase","bisonS","",497,1,20.153,1.493,12.042,17.519,9.859,19.517,4.531,14.322,13.879,24.062,4.708,7.41,11.662,6.672,15.099,12.678,10.928,19.141,3.519,8.519
-"peptidase","bisonR","",612,1,27.964,1.722,12.894,19.021,9.912,22.132,5.479,12.719,8.954,30.214,4.993,7.725,15.943,9.861,20.652,12.475,13.515,20.033,4.533,9.088
-"peptidase","bisonQ","",1064,1,26.028,1.784,12.69,15.317,9.222,20.119,5.567,12.978,7.626,26.305,4.822,7.545,14.358,10.104,17.995,12.93,13.752,17.482,3.949,8.602
-"peptidase","bisonP","",990,1,25.312,1.856,12.346,15.217,8.714,19.308,5.467,12.647,6.953,25.637,4.778,7.121,14.083,9.651,18.093,12.07,13.104,17.332,3.829,8.007
-"ribosomal","bisonN","",597,1,10.01,0.965,5.385,10.951,4.327,10.544,2.581,8.779,14.353,12.692,2.93,3.851,6.58,3.899,10.67,5.492,5.36,12.844,1.343,4.457
-"ribosomal","bisonS","",716,1,9.582,0.75,4.747,9.605,3.521,9.709,2.461,7.993,12.284,11.105,2.788,3.325,6.226,3.719,11.166,5.324,5.275,11.814,1.208,3.87
-"ribosomal","bisonR","",543,1,10.785,0.726,4.842,9.827,3.503,10.158,2.735,7.867,11.309,11.521,2.691,3.694,6.694,4.481,12.494,5.14,5.902,10.91,1.168,3.462
-"ribosomal","bisonQ","",882,1,11.863,0.87,5.268,9.034,3.349,9.821,2.951,7.934,9.705,11.274,2.967,3.89,6.298,5.355,12.477,5.797,6.717,10.444,1.177,3.102
-"ribosomal","bisonP","",860,1,11.72,0.887,5.187,9.138,3.386,10.077,2.973,7.877,9.765,11.305,2.865,3.815,6.47,5.167,12.776,5.78,6.442,10.681,1.194,3.364
-"protease","bisonN","",377,1,19.454,1.554,10.708,17.931,11.215,20.926,3.687,16.984,14.804,27.785,5.122,7.963,11.676,6.894,13.899,13.658,10.692,20.743,2.706,9.029
-"protease","bisonS","",470,1,19.645,1.515,10.268,16.328,9.5,18.498,3.385,15.411,12.409,24.491,4.428,7.33,10.977,7.015,13.434,12.296,9.755,19.128,2.717,7.4
-"protease","bisonR","",418,1,27.6,1.457,11.859,16.725,9.294,21.737,4.258,13.694,9.45,30.093,4.593,7.433,15.108,10.325,18.203,11.792,12.301,20.799,3.639,8.148
-"protease","bisonQ","",930,1,25.572,1.696,12.102,14.799,8.734,20.469,4.405,14.098,7.323,27.489,4.732,7.535,13.888,10.513,17.848,12.922,12.725,19.148,3.545,6.825
-"protease","bisonP","",734,1,25.296,1.471,11.764,14.46,8.307,19.868,4.256,13.463,7.315,26.264,4.681,7.356,13.522,10.012,17.403,12.008,12.163,19.114,3.456,6.674
-" reductase","bisonN","",536,1,18.961,4.028,11.519,20.405,10.235,19.69,4.722,15.506,17.451,24.302,5.646,8.237,11.116,6.349,13.843,12.498,10.64,19.886,3.19,9.623
-" reductase","bisonS","",531,1,19.207,3.522,10.25,17.416,8.889,17.94,4.377,13.343,13.638,21.166,4.949,6.798,10.339,6.213,13.348,11.205,9.917,18.337,3.055,7.331
-" reductase","bisonR","",378,1,20.796,2.677,9.362,15.548,7.762,17.132,4.741,11.058,8.614,21.492,4.511,5.622,11.167,6.841,15.138,9.257,9.849,16.696,2.894,7.04
-" reductase","bisonQ","",785,1,24.408,3.29,11.14,15.006,8.688,18.804,5.968,13.118,8.454,22.766,5.082,6.679,12.162,9.043,16.046,11.373,12.434,17.525,3.299,6.913
-" reductase","bisonP","",675,1,24.147,3.033,10.738,14.644,8.332,18.041,5.424,12.698,8.09,21.997,4.964,6.717,11.539,8.807,15.856,10.612,11.821,17.304,3.102,6.804
-"transposase","bisonN","",471,1,17.076,1.399,7.898,18.423,7.471,13.072,5.507,12.711,24.958,26.503,3.741,8.8,7.361,7.809,17.047,11.573,10.161,15.412,4.824,9.482
-"transposase","bisonS","",425,1,16.892,1.772,8.365,16.546,7.511,13.445,5.139,12.271,22.064,24.04,4.122,8.125,7.84,6.828,18.668,11.336,9.304,14.904,4.734,8.744
-"transposase","bisonR","",314,1,18.914,1.796,7.506,15.955,7.003,17.162,4.803,6.764,14.283,26.309,3.618,5.516,9.933,6.911,21.618,10.439,7.971,15.646,4.494,7.226
-"transposase","bisonQ","",1085,1,18.263,4.134,8.288,10.426,6.362,12.923,5.043,9.029,12.761,18.747,3.159,7.355,8.219,10.573,20.88,11.635,9.959,13.338,3.713,5.854
-"transposase","bisonP","",550,1,16.042,3.642,7.653,10.522,6.365,12.027,5.104,8.178,11.295,18.916,3.509,5.855,8.091,8.584,18.289,9.909,8.798,13.042,3.853,5.596
-"periplasmic","bisonN","",313,1,18.473,1.038,12.304,15.441,10.502,17.438,3.144,13.565,15.693,24.131,4.505,7.968,13.077,7.505,13.137,12.396,10.629,19.214,3.042,10.326
-"periplasmic","bisonS","",409,1,20.159,1.23,11.621,14.667,9.306,17.716,2.905,13.553,14.205,22.007,4.205,7.501,12.716,7.672,12.883,12.24,10.746,19.467,3.249,8.614
-"periplasmic","bisonR","",440,1,22.902,1.12,12.064,14.055,9.502,19.802,3.234,11.616,10.386,24.632,4.159,7.048,14.766,9.65,17.727,10.934,11.755,18.757,3.959,8.277
-"periplasmic","bisonQ","",850,1,25.292,1.418,13.372,13.453,9.034,19.272,3.292,12.875,8.955,23.404,4.208,8.376,14.853,10.484,15.908,12.673,13.488,18.094,3.978,7.245
-"periplasmic","bisonP","",772,1,24.144,1.339,12.953,12.882,8.589,18.782,3.276,12.034,8.744,22.184,4.133,7.948,14.29,9.956,15.784,12.199,12.912,17.553,3.965,7.153
-"signal","bisonN","",297,1,18.165,1.852,12.586,18.966,11.694,17.747,3.387,14.865,17.347,26.889,4.966,8.024,10.956,6.875,14.603,13.195,10.717,20.047,2.391,8.593
-"signal","bisonS","",408,1,18.223,1.855,10.838,15.23,8.821,16.436,3.527,12.441,12.466,22.679,4.407,6.549,10.115,6.586,14.525,10.885,10.11,18.191,2.691,5.993
-"signal","bisonR","",299,1,25.181,1.896,11.134,19.144,9.087,19.813,4.839,12.334,10.14,32.217,5.037,6.244,12.809,11.037,19.913,11.234,12.555,19.04,3.284,6.054
-"signal","bisonQ","",732,1,25.425,2.034,12.243,16.406,8.213,18.031,5.303,14.452,7.981,29.495,4.984,7.357,12.855,12.869,18.719,13.464,13.714,18.519,3.143,5.496
-"signal","bisonP","",641,1,23.841,1.93,11.376,15.476,7.746,16.665,5.027,13.732,7.173,28.257,4.927,6.877,11.594,11.892,18.028,12.516,12.719,17.493,2.816,4.952
-"phosphatase","bisonN","",364,1,15.077,1.761,11.187,16.135,9.159,15.843,4.052,11.255,12.462,22.055,3.747,5.478,9.03,4.253,11.808,10.148,8.332,16.382,2.508,7.291
-"phosphatase","bisonS","",372,1,15.065,1.554,9.559,14.817,8.091,14.712,3.586,10.194,10.605,19.575,3.495,4.656,7.995,4.051,11.269,9.056,7.554,15.215,2.352,5.586
-"phosphatase","bisonR","",324,1,19.599,1.321,9.056,13.978,7.269,16.281,4.386,9.611,7.355,22.256,3.84,4.617,9.87,5.79,12.926,8.395,8.577,13.978,2.769,5.707
-"phosphatase","bisonQ","",642,1,21.611,2.195,10.724,12.88,6.941,16.322,4.883,10.908,5.777,21.86,4.241,5.204,10.332,7.777,14.927,9.96,10.382,14.522,2.843,5.556
-"phosphatase","bisonP","",558,1,21.842,1.909,10.256,12.24,6.808,16.332,4.876,10.871,5.297,21.597,4.073,5.335,9.686,7.634,14.124,9.919,9.815,14.787,2.794,5.292
Deleted: pkg/CHNOSZ/inst/extdata/protein/DS13.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/DS13.csv 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/inst/extdata/protein/DS13.csv 2020-07-13 02:30:55 UTC (rev 557)
@@ -1,34 +0,0 @@
-"protein","organism","ref","abbrv","chains","Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys","Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val","Trp","Tyr"
-"bisonN","Aquificae",15878,"638303(6231)",1,15.29,2.26,11.16,21.74,12.14,17.19,4.17,15.82,19.7,28.6,4.84,7.82,10.25,6.77,13.73,13.15,9.84,18.96,2.64,9.88
-"bisonN","Crenarchaeota",5712,"1104324(1060)",1,19.98,1.66,8.81,13.77,6.87,14.99,3.32,9.84,9.96,20.93,3.7,4.67,9.92,4.17,14.26,9.4,8.97,19.62,2.89,7.96
-"bisonN","Proteobacteria",4462,"1177927(716)",1,17.42,1.69,9.38,10.43,7.35,13.76,3.71,10.12,7.99,18.81,4.35,6.18,8.31,6.63,10.98,10.21,9.13,12.87,2.63,5.25
-"bisonN","Deinococcus-Thermus",1668,"498848(1260)",1,17.19,0.8,6.49,13.76,6.45,15.09,3.18,6.07,7.04,22.38,2.87,3.34,10.47,4.31,13.38,6.89,6.88,13.04,2.38,5.08
-"bisonN","Firmicutes",1181,"246194(38)",1,15.39,1.66,10.18,17.36,10.03,15.18,3.6,15.43,14.01,22.31,4.07,7.28,9.64,5.61,13.55,11.18,9.25,16.01,2.7,7.27
-"bisonS","Aquificae",9549,"608538(3683)",1,14.34,2.13,10.38,19.99,11.12,15.92,3.85,14.67,18.13,26.09,4.55,7.32,9.55,6.31,12.82,12.21,9.16,17.72,2.51,9.04
-"bisonS","Crenarchaeota",7646,"1104324(1115)",1,19.19,1.6,8.94,14.37,6.83,15.38,3.3,10.45,9.9,21.18,3.79,4.75,9.8,4.01,14.73,9.96,8.91,19.65,2.88,7.75
-"bisonS","Proteobacteria",6195,"1177927(596)",1,18.43,1.73,9.52,10.94,7.55,14.25,3.72,10.46,7.93,19.32,4.29,5.73,8.93,6.46,11.81,10.08,9.21,13.57,2.79,5.1
-"bisonS","Firmicutes",3872,"406124(401)",1,17.55,1.94,10.11,16.2,9.07,15.47,4.13,13.72,11.81,22.32,4.45,6.52,10.03,6.88,13.67,10.69,10.04,16.84,2.96,6.05
-"bisonS","Deinococcus-Thermus",1986,"498848(1392)",1,17.89,0.9,6.7,14.24,6.5,15.16,3.27,6.39,7.16,23.02,2.93,3.4,10.57,4.64,13.79,6.86,6.84,13.18,2.47,5.05
-"bisonS","Euryarchaeota",1301,"589924(72)",1,15.66,1.92,9.45,15.61,7.95,15.26,3.47,12.82,10.98,21.12,4.01,6.01,9.3,4.67,14.66,11.32,9.17,17.28,2.58,6.64
-"bisonS","Chloroflexi",1237,"926569(221)",1,20.14,1.91,9.87,15.25,8.14,16.5,4.05,11.61,8.03,22.58,4.27,5.26,11.81,6.86,16.17,9.39,10.01,16.73,3.51,5.88
-"bisonR","Deinococcus-Thermus",8493,"498848(6227)",1,22.34,0.95,7.5,16.6,7.49,18.37,3.9,6.12,7.51,28.36,3.23,3.52,12.98,5.56,16.76,7.67,7.95,15.74,3.03,5.94
-"bisonR","Firmicutes",5406,"406124(728)",1,22.59,2.1,11.12,16.32,8.3,16.89,5.1,13.23,8.88,25.04,4.96,6.71,12.17,9.44,16.92,10.43,11.98,17.63,2.99,7.13
-"bisonR","Proteobacteria",3078,"1177927(159)",1,21.72,1.99,9.66,13.01,7.86,15.64,4.35,11.02,7.37,23.41,4.39,6.01,10.97,8.76,14.84,10.19,10.69,15.47,3.35,6.13
-"bisonR","Aquificae",2935,"608538(1069)",1,12.85,1.87,9,16.56,9.28,13.69,3.38,12.43,14.62,22.28,3.91,6.22,8.34,5.69,11.28,10.3,7.98,14.99,2.14,7.54
-"bisonR","Bacteroidetes",2624,"518766(511)",1,21.31,1.87,9.68,14.79,8.41,16.78,4.88,11.43,6.99,25.08,3.88,5.89,12.61,9.42,17.11,10.78,11.5,15.71,4.06,8.21
-"bisonR","Chloroflexi",2493,"309801(1008)",1,23.66,2.06,10.55,14.98,7.73,16.63,4.79,10.78,5.55,24.55,4.34,4.85,12.63,8.23,18.14,9.38,10.97,16.83,3.84,6.29
-"bisonR","Cyanobacteria",1134,"321327(63)",1,24.5,2.33,11.74,15.64,8.3,17.51,4.93,11.46,7.32,26.54,4.24,6.71,13.26,10.18,18.97,11.52,12.07,17.67,4.59,7.49
-"bisonQ","Chloroflexi",19149,"357808(12210)",1,24.64,1.98,11.33,11.99,7.27,16.25,4.69,12,4.32,23.16,4.48,5.48,11.95,8,17.32,10.29,11.88,16.21,3.36,5.8
-"bisonQ","Cyanobacteria",15593,"321332(9106)",1,20.5,2.39,9.34,12.85,7.22,16.2,4.42,10.34,6.49,25.29,3.7,5.61,12.34,11.91,15.03,11.45,10.29,14.96,3.9,5.75
-"bisonQ","Proteobacteria",8135,"1177927(1539)",1,20.1,2.07,9.97,11.73,7.57,14.98,4.38,10.85,7.57,21.44,4.77,6.57,9.59,8.16,13.13,10.92,10.7,14.54,3.11,5.57
-"bisonQ","Acidobacteria",5209,"981222(4598)",1,29.91,2.82,12.79,16.45,10.8,20.73,5.65,13,8,29.43,4.97,7.67,15.47,10.46,21.31,13.33,16.05,20.76,4.05,7.47
-"bisonQ","Firmicutes",4474,"635013(127)",1,20.9,2.08,9.84,13.97,7.1,15.12,4.75,11.36,7.2,22.09,4.3,5.71,10.98,8.59,15.91,9.5,10.59,15.65,2.69,6.2
-"bisonQ","Bacteroidetes",3036,"518766(252)",1,19.8,1.88,9.59,13.26,8.67,15.89,4.63,11.69,7.92,22.48,3.85,6.88,11.63,8.76,14.7,11.37,11.74,14.56,3.58,7.91
-"bisonQ","Chlorobi",2477,"517418(2056)",1,19.19,1.92,10.14,15.02,9.67,13.54,4.47,13.87,12.31,22.61,4.62,7.55,9.05,8.33,12.95,12.77,11.63,14.52,2.07,6.89
-"bisonP","Chloroflexi",17557,"357808(7686)",1,24.53,2,11.31,12.29,7.5,16.43,4.76,12.52,4.62,23.98,4.53,5.81,12.17,8.47,17.26,10.64,12.15,16.46,3.46,6.09
-"bisonP","Proteobacteria",8385,"1177927(1591)",1,20.39,2.1,9.96,11.78,7.61,15.02,4.34,10.83,7.5,21.69,4.82,6.55,9.79,8.38,13.2,10.97,10.7,14.84,3.14,5.7
-"bisonP","Cyanobacteria",8158,"321327(4146)",1,20.52,2.24,9.04,12.7,6.88,15.38,4.12,9.64,6.06,24.47,3.48,5.34,11.86,11.05,14.97,10.58,9.66,14.54,3.75,5.69
-"bisonP","Firmicutes",5590,"635013(184)",1,23.2,2.16,10.69,15.13,7.4,16.46,5.05,12.02,7.24,24.15,4.57,5.91,12.16,9.27,17.61,9.61,11.47,17.25,2.86,6.51
-"bisonP","Acidobacteria",3500,"981222(2912)",1,23.18,2.25,10.04,13.44,8.45,16.16,4.58,10.46,6.55,23.16,4.05,5.96,11.96,8.28,17.07,10.47,12.17,16.09,3.21,6.06
-"bisonP","Bacteroidetes",2373,"518766(313)",1,20.59,2.07,9.62,13.47,8.31,16.26,4.7,11.13,7.19,23.09,3.96,6.57,11.74,8.67,15.67,11.07,11.54,15.32,3.85,7.75
-"bisonP","Deinococcus-Thermus",2181,"498848(834)",1,19.19,1.39,7.44,12.94,6.43,14.75,3.9,6.91,5.96,21.84,3.19,3.85,10.87,6.33,14.53,7.71,7.84,13.35,2.84,5.34
Copied: pkg/CHNOSZ/inst/extdata/protein/EF-Tu.aln (from rev 556, pkg/CHNOSZ/inst/extdata/fasta/EF-Tu.aln)
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/EF-Tu.aln (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/EF-Tu.aln 2020-07-13 02:30:55 UTC (rev 557)
@@ -0,0 +1,64 @@
+>EFTU1_ML-stem
+MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLALKGLAEAKAYDQIDKAPEEKARG
+ITINIAHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLARQVGVPYIVVFINKVDMVDDPELLELVEMEVRDLLSKYEFPGDEVPVIRGSALKALE
+APQKWYEKILELLDAVDEYIPTPERDVDKPFLMPIEDVFSITGRGTVVTGRIERGVIKPG
+DEVEIVGLSETKKTTVTSVEMFRKLLDEGIAGDNVGVLLRGIDKEEVERGQVLAKPGSIT
+PHTKFKAQVYVLKKEEGGRHTPFFNGYRPQFYFRTTDVTGIVELPEGVEMVMPGDNVEMT
+VELIYPIAMEEGLRFAIREGGRTVGAGVVTKIIE
+>EFTU1_Alt-stem
+MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITKVLSLKGLAEAKAYDQIDNAPEEKARG
+ITINITHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHV
+LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDVPVIRGSALKALE
+GDNEWYKPILELMDAVDNYIPDPERDVDKPFLMPIEDVFSITGRGTVVTGRIERGVIKPG
+DEVEIVGLKETKKTTVTSVEMFRKLLDEGQAGDNVGCLLRGIEKEEVERGQVLAKPGSIT
+PHTKFEAQVYVLKKEEGGRHTPFFNNYRPQFYFRTTDVTGIVELPEGVEMVMPGDNVEMT
+VELIYPIAIEEGLRFAIREGGRTVGAGVVTKIIE
+>EFTU1_ML-meso
+MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVLAKKGLAEARAYDQIDNAPEEKERG
+ITINISHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLARQVGVPYIVVALNKCDMVDDEELLELVEMEVRELLSSYDFDGDDTPVIRVSALKALE
+GDEKWVEKILELMDAVDEYIPTPERDTDKPFLMPIEDVFTITGRGTVVTGRVERGVLKVG
+DEVEIVGIKETQKTTVTGIEMFRKLLDEAQAGDNVGLLLRGIKREDVERGQVLAKPGSIT
+PHTKFEAEVYVLSKEEGGRHTPFFNNYRPQFYFRTTDVTGVITLPEGTEMVMPGDNVEMT
+VELIAPIAMEEGLRFAIREGGRTVGAGRVTKIIK
+>EFTU1_ECOLI
+MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
+ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
+GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
+EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
+PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
+VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS
+>EFTU1_THETH
+MAKGEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENNVEVKDYGDIDKAPEERARG
+ITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHI
+LLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALE
+QMHEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVG
+DEVEIVGLAETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSIT
+PHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFT
+VELIKPVALEEGLRFAIREGGRTVGAGVVTKILE
+>EFTU_THEMA
+MAKEKFVRTKPHVNVGTIGHIDHGKSTLTAAITKYLSLKGLAQYIPYDQIDKAPEEKARG
+ITINITHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHV
+LLARQVEVPYMIVFINKTDMVDDPELIDLVEMEVRDLLSQYGYPGDEVPVIRGSALKAVE
+APNEAYKPIQELLDAMDNYIPDPQRDVDKPFLMPIEDVFSITGRGTVVTGRIERGRIRPG
+DEVEIIGLSEIKKTVVTSVEMFRKELDEGIAGDNVGCLLRGIDKDEVERGQVLAAPGSIK
+PHKRFKAQIYVLKKEEGGRHTPFTKGYKPQFYIRTADVTGIVGLPEGVEMVMPGDHVEME
+IELIYPVAIEKGQRFAVREGGRTVGAGVVTEVIE
+>EFTU1_ML-stem-DE
+MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLALKGLAEAKAYEQIDKAPEEKARG
+ITINIAHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLARQVGVPYIVVFINKVDMVDDPELLELVEMEVRDLLSKYEFPGDEVPVIRGSALKALE
+APQKWYEKILELLDAVDEYIPTPERDVDKPFLMPIEDVFSITGRGTVVTGRIERGVIKPG
+DEVEIVGLSETKKTTVTSVEMFRKLLDEGIAGDNVGVLLRGIDKEEVERGQVLAKPGSIT
+PHTKFKAQVYVLKKEEGGRHTPFFNGYRPQFYFRTTDVTGIVELPEGVEMVMPGDNVEMT
+VELIYPIAMEEGLRFAIREGGRTVGAGVVTKIIE
+>EFTU1_ML-stem-DE-ST
+MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLALKGLAEAKAYEQIDKAPEEKARG
+ITINIAHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLARQVGVPYIVVFINKVDMVDDPELLELVEMEVRDLLSKYEFPGDEVPVIRGTALKALE
+APQKWYEKILELLDAVDEYIPTPERDVDKPFLMPIEDVFSITGRGTVVTGRIERGVIKPG
+DEVEIVGLSETKKTTVTSVEMFRKLLDEGIAGDNVGVLLRGIDKEEVERGQVLAKPGSIT
+PHTKFKAQVYVLKKEEGGRHTPFFNGYRPQFYFRTTDVTGIVELPEGVEMVMPGDNVEMT
+VELIYPIAMEEGLRFAIREGGRTVGAGVVTKIIE
Added: pkg/CHNOSZ/inst/extdata/protein/POLG.csv
===================================================================
(Binary files differ)
Index: pkg/CHNOSZ/inst/extdata/protein/POLG.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/POLG.csv 2020-07-12 00:00:38 UTC (rev 556)
+++ pkg/CHNOSZ/inst/extdata/protein/POLG.csv 2020-07-13 02:30:55 UTC (rev 557)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 557
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