[CHNOSZ-commits] r729 - in pkg/CHNOSZ: . demo inst inst/extdata/protein man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 20 07:20:16 CEST 2022
Author: jedick
Date: 2022-06-20 07:20:16 +0200 (Mon, 20 Jun 2022)
New Revision: 729
Added:
pkg/CHNOSZ/demo/rank_affinity.R
pkg/CHNOSZ/inst/extdata/protein/TBD+05.csv
pkg/CHNOSZ/inst/extdata/protein/TBD+05_aa.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/rank_affinity.Rd
Log:
Add demo/rank_affinity.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-06-20 02:29:42 UTC (rev 728)
+++ pkg/CHNOSZ/DESCRIPTION 2022-06-20 05:20:16 UTC (rev 729)
@@ -1,6 +1,6 @@
Date: 2022-06-20
Package: CHNOSZ
-Version: 1.9.9-21
+Version: 1.9.9-22
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/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2022-06-20 02:29:42 UTC (rev 728)
+++ pkg/CHNOSZ/demo/00Index 2022-06-20 05:20:16 UTC (rev 729)
@@ -30,3 +30,4 @@
comproportionation Gibbs energy of sulfur comproportionation
Pourbaix Eh-pH diagram for Fe-O-H with equisolubility lines
E_coli Gibbs energy of biomass synthesis in E. coli
+rank_affinity Affinity ranking for proteins in yeast nutrient limitation
Added: pkg/CHNOSZ/demo/rank_affinity.R
===================================================================
--- pkg/CHNOSZ/demo/rank_affinity.R (rev 0)
+++ pkg/CHNOSZ/demo/rank_affinity.R 2022-06-20 05:20:16 UTC (rev 729)
@@ -0,0 +1,30 @@
+## Affinity ranking for proteins coded by differentially expressed
+## genes in response to carbon limitation in yeast
+# Demo written on 20220620
+# Adapted from an example previously in read.expr.Rd (CHNOSZ 1.1.0) and yeast.Rd (CHNOSZ 1.2.0-1.3.0)
+library(CHNOSZ)
+
+# Experimental data are from Tai et al. (2005)
+file <- system.file("extdata/protein/TBD+05.csv", package = "CHNOSZ")
+dat <- read.csv(file, row.names = 1, check.names = FALSE)
+
+# The activities of ammonium and sulfate used here
+# are similar to the non-growth-limiting concentrations
+# used by Boer et al. (2003)
+basis(c("glucose", "H2O", "NH4+", "oxygen", "SO4-2", "H+"),
+ c(-1, 0, -1.3, 999, -1.4, -7))
+
+aafile <- system.file("extdata/protein/TBD+05_aa.csv", package = "CHNOSZ")
+aa <- read.csv(aafile)
+iprotein <- add.protein(aa, as.residue = TRUE)
+
+res <- 200
+aout <- affinity(C6H12O6 = c(-60, -20, res), O2 = c(-72, -60, res), iprotein = iprotein)
+groups <- apply(dat, 2, which)
+names(groups) <- paste0(names(groups), "\n(", colSums(dat), ")")
+arank <- rank_affinity(aout, groups)
+fill <- c("#d2b48c", "#b0e0e6", "#d3d3d3", "#d8bfd8")
+diagram(arank, format.names = FALSE, fill = fill)
+
+title(main = paste("Affinity ranking for proteins coded by differentially expressed\n",
+ "genes under carbon limitation in yeast (data from Tai et al., 2005)"), font.main = 1)
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2022-06-20 02:29:42 UTC (rev 728)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-06-20 05:20:16 UTC (rev 729)
@@ -10,7 +10,7 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.9.9-21 (2022-06-08)}{
+\section{Changes in CHNOSZ version 1.9.9-22 (2022-06-20)}{
\subsection{MAJOR CHANGE}{
\itemize{
@@ -68,10 +68,10 @@
\item Add a check to \code{add.protein()} that all new protein IDs
(protein name + organism name) are unique.
- \item Add function \code{rank_affinity()} to calculate (sums of ranks of
- affinities for species in designated groups) normalized by number of
- species in each group. The output of the new function can be used by
- \code{diagram()}.
+ \item Add function and demo for \code{rank_affinity()} to calculate (sums
+ of ranks of affinities for species in designated groups) normalized by
+ number of species in each group. The output of the new function can be
+ used by \code{diagram()}.
}
}
Added: pkg/CHNOSZ/inst/extdata/protein/TBD+05.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/TBD+05.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/TBD+05.csv 2022-06-20 05:20:16 UTC (rev 729)
@@ -0,0 +1,393 @@
+protein,down.in.Clim-aerobic,up.in.Clim-aerobic,down.in.Clim-anaerobic,up.in.Clim-anaerobic
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Added: pkg/CHNOSZ/inst/extdata/protein/TBD+05_aa.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/protein/TBD+05_aa.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/protein/TBD+05_aa.csv 2022-06-20 05:20:16 UTC (rev 729)
@@ -0,0 +1,393 @@
+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
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+YCL025C,Sce,S000000530,AGP1,1,63,11,25,29,40,56,13,52,27,60,15,22,21,23,24,47,30,38,12,25
+YCR043C,Sce,S000000639,,1,3,5,12,5,9,9,4,8,10,12,3,3,5,2,2,10,5,7,4,9
+YCR102C,Sce,S000000699,,1,31,3,20,22,12,32,8,28,27,32,1,20,20,13,12,17,18,35,3,14
+YDR309C,Sce,S000002717,GIC2,1,17,1,20,20,17,11,11,16,31,32,5,32,23,16,20,69,23,9,1,9
+YDR352W,Sce,S000002760,YPQ2,1,20,6,11,19,17,23,3,23,8,42,3,14,14,14,13,33,22,12,3,17
+YDR533C,Sce,S000002941,HSP31,1,24,1,23,11,15,21,5,11,23,17,1,10,9,3,4,13,17,19,2,8
+YEL016C,Sce,S000000742,NPP2,1,19,5,36,30,28,27,15,40,30,44,19,33,29,15,20,27,18,25,10,23
+YER001W,Sce,S000000803,MNN1,1,43,10,52,52,47,34,24,42,65,66,11,46,30,25,36,46,47,39,13,34
+YER028C,Sce,S000000830,MIG3,1,19,6,19,12,14,20,14,21,21,21,6,24,31,14,30,65,28,22,0,7
+YER053C,Sce,S000000855,PIC2,1,20,8,5,12,15,26,3,20,27,23,12,10,13,13,7,22,19,21,6,18
+YER124C,Sce,S000000926,DSE1,1,15,15,44,20,24,33,11,47,46,58,14,46,21,23,9,61,36,27,7,16
+YFL025C,Sce,S000001869,BST1,1,52,9,47,51,67,41,24,87,51,135,25,66,46,32,38,90,53,57,15,43
+YFL026W,Sce,S000001868,STE2,1,30,2,22,12,27,18,4,33,17,44,11,23,15,14,16,49,45,27,3,19
+YGL065C,Sce,S000003033,ALG2,1,30,6,22,37,37,22,10,43,37,53,8,25,19,19,15,32,23,33,7,25
+YGR041W,Sce,S000003273,BUD9,1,26,4,31,32,26,36,13,39,26,34,14,35,34,22,32,69,33,24,3,14
+YGR125W,Sce,S000003357,,1,57,12,48,53,61,63,18,97,52,118,24,60,38,31,48,85,54,64,11,42
+YGR192C,Sce,S000003424,TDH3,1,32,2,24,15,10,26,8,19,26,21,7,13,12,5,11,26,24,37,3,11
+YHR048W,Sce,S000001090,YHK8,1,40,10,14,21,41,37,10,45,22,52,20,9,21,10,23,39,38,28,8,26
+YHR049W,Sce,S000001091,FSH1,1,14,1,17,17,11,14,8,19,23,19,5,8,14,10,6,21,7,18,2,9
+YHR179W,Sce,S000001222,OYE2,1,36,0,21,31,17,34,8,23,26,29,5,25,24,13,22,18,16,24,8,20
+YHR210C,Sce,S000001253,,1,20,4,25,18,12,24,6,19,23,32,6,23,13,6,14,25,27,24,1,19
+YIL111W,Sce,S000001373,COX5B,1,9,0,4,11,5,13,1,5,14,18,3,9,8,6,9,8,12,6,6,4
+YJL212C,Sce,S000003748,OPT1,1,47,12,29,25,60,47,12,59,42,71,22,46,43,22,26,52,49,64,26,45
+YJL213W,Sce,S000003749,,1,29,9,18,20,13,35,6,22,22,32,10,10,12,12,15,17,20,18,0,11
+YJR030C,Sce,S000003791,,1,24,11,53,39,27,23,14,46,55,92,15,39,28,21,35,106,37,47,5,28
+YKL043W,Sce,S000001526,PHD1,1,29,2,12,19,9,12,10,23,18,25,8,25,34,19,18,32,31,24,2,14
+YKL062W,Sce,S000001545,MSN4,1,42,4,41,26,28,17,21,28,39,40,16,70,36,25,25,92,49,19,3,9
+YKL209C,Sce,S000001692,STE6,1,73,26,53,66,61,76,24,111,73,151,37,67,24,52,53,114,95,76,15,43
+YKR093W,Sce,S000001801,PTR2,1,45,12,26,34,51,36,8,54,34,43,18,25,34,17,13,44,32,33,13,29
+YLL028W,Sce,S000003951,TPO1,1,59,12,18,26,40,48,11,43,21,58,21,19,33,8,20,35,33,46,9,26
+YLR108C,Sce,S000004098,,1,17,15,22,38,28,23,15,34,43,52,5,29,19,14,19,35,27,30,3,17
+YLR179C,Sce,S000004169,,1,14,2,16,11,7,16,3,15,15,12,6,11,13,4,3,14,12,13,2,12
+YLR460C,Sce,S000004452,,1,30,4,21,22,11,31,8,35,32,33,2,20,20,13,10,17,16,34,3,14
+YMR057C,Sce,S000004661,,1,6,6,4,3,7,7,4,10,4,10,1,3,9,1,18,10,8,5,1,6
+YMR269W,Sce,S000004882,TMA23,1,9,0,14,17,5,18,6,5,50,11,1,9,3,1,13,28,6,8,4,3
+YMR285C,Sce,S000004898,NGL2,1,23,10,35,39,24,30,19,18,50,42,14,26,24,21,26,33,21,33,8,19
+YNL066W,Sce,S000005010,SUN4,1,35,11,24,18,7,41,3,17,13,21,3,18,16,13,4,68,48,32,7,21
+YNL134C,Sce,S000005078,,1,33,4,26,23,14,30,8,32,34,32,5,14,20,13,9,17,17,30,3,12
+YNR032C-A,Sce,S000007251,HUB1,1,1,1,6,5,1,5,2,4,8,10,1,3,1,4,2,4,2,10,0,3
+YOL136C,Sce,S000005496,PFK27,1,13,8,26,23,32,14,12,29,22,36,4,36,13,12,14,48,24,16,0,15
+YOR171C,Sce,S000005697,LCB4,1,28,12,42,38,24,33,12,44,52,61,13,43,37,15,21,60,34,33,5,17
+YPL095C,Sce,S000006016,EEB1,1,27,6,21,30,26,30,16,14,30,48,5,25,23,12,21,31,34,30,9,18
+YPR013C,Sce,S000006217,CMR3,1,11,8,9,13,8,12,9,14,22,20,10,23,31,15,11,39,28,18,2,14
+YPR106W,Sce,S000006310,ISR1,1,23,6,21,20,22,16,15,27,24,55,10,26,25,15,13,58,25,20,4,18
+YPR138C,Sce,S000006342,MEP3,1,48,11,19,17,26,48,10,33,18,48,14,21,11,10,13,36,31,34,17,24
+YAL054C,Sce,S000000050,ACS1,1,56,7,48,38,26,50,20,44,47,58,8,23,40,22,30,51,47,55,12,31
+YAR068W,Sce,S000000091,,1,7,0,1,0,6,0,8,1,6,41,3,4,25,14,3,10,17,12,3,0
+YBR026C,Sce,S000000230,ETR1,1,19,2,21,19,11,24,5,25,37,32,6,24,14,14,10,41,28,29,6,13
+YBR046C,Sce,S000000250,ZTA1,1,25,2,15,23,13,27,2,25,34,32,3,12,14,10,9,23,17,25,1,22
+YBR068C,Sce,S000000272,BAP2,1,50,10,23,24,45,48,11,52,30,54,17,26,19,16,22,55,29,39,10,29
+YBR072W,Sce,S000000276,HSP26,1,11,0,21,12,11,15,3,9,20,16,1,18,14,5,8,16,7,18,2,7
+YBR116C,Sce,S000000320,,1,5,10,4,7,14,5,1,11,12,23,4,6,3,10,7,19,16,9,3,6
+YBR117C,Sce,S000000321,TKL2,1,53,3,41,41,30,61,18,35,40,57,12,26,34,27,28,59,34,44,9,29
+YBR150C,Sce,S000000354,TBS1,1,46,19,99,78,62,28,29,57,81,112,25,86,35,27,54,94,61,53,7,41
+YBR157C,Sce,S000000361,ICS2,1,7,2,11,18,15,14,9,13,22,16,3,14,12,9,16,47,14,5,0,8
+YBR230C,Sce,S000000434,OM14,1,15,5,6,4,4,7,6,3,12,16,1,11,3,3,3,13,6,9,0,7
+YBR295W,Sce,S000000499,PCA1,1,75,42,54,76,39,88,29,95,77,96,19,51,34,31,55,136,80,109,6,24
+YCR010C,Sce,S000000603,ADY2,1,30,3,10,11,23,30,4,14,7,33,5,17,12,6,7,16,17,19,5,14
+YCR018C,Sce,S000000611,SRD1,1,11,7,11,17,3,8,1,11,28,12,2,18,6,8,21,24,15,8,3,7
+YDL009C,Sce,S000002167,,1,4,4,3,1,16,3,6,8,7,13,2,6,5,2,5,7,2,8,1,4
+YDL049C,Sce,S000002207,KNH1,1,26,3,12,7,10,13,4,15,14,16,8,14,13,10,11,15,36,22,4,15
+YDL085W,Sce,S000002243,NDE2,1,35,2,26,35,27,31,7,32,43,58,17,22,24,20,23,38,38,38,7,22
+YDL204W,Sce,S000002363,RTN2,1,20,0,21,23,15,18,12,25,30,33,7,33,19,13,21,35,31,23,1,13
+YDL214C,Sce,S000002373,PRR2,1,31,13,45,45,27,30,18,53,47,50,13,46,22,15,36,85,48,42,5,28
+YDL223C,Sce,S000002382,HBT1,1,67,0,83,61,18,75,47,30,83,23,17,84,56,44,33,141,103,41,3,37
+YDR018C,Sce,S000002425,,1,20,7,13,16,28,19,8,28,33,48,9,25,14,17,17,27,19,22,7,19
+YDR034W-B,Sce,S000007234,,1,1,9,1,1,2,2,4,1,0,4,2,2,5,6,4,1,1,3,0,2
+YDR070C,Sce,S000002477,FMP16,1,5,0,9,6,4,5,2,2,11,8,3,5,6,5,9,4,5,2,0,2
+YDR077W,Sce,S000002484,SED1,1,24,6,8,22,5,16,1,9,8,15,2,14,33,2,0,42,99,22,0,10
+YDR216W,Sce,S000002624,ADR1,1,57,22,86,75,75,46,37,74,86,147,29,120,48,37,61,151,71,48,4,49
+YDR256C,Sce,S000002664,CTA1,1,35,5,31,23,30,34,17,27,27,27,8,37,33,33,26,29,30,32,8,23
+YDR380W,Sce,S000002788,ARO10,1,33,12,35,35,30,42,14,47,42,56,14,45,25,24,21,49,31,45,6,29
+YDR384C,Sce,S000002792,ATO3,1,16,9,13,7,22,28,2,13,5,38,8,16,10,6,7,25,21,13,5,11
+YDR453C,Sce,S000002861,TSA2,1,17,2,12,12,11,14,2,12,18,18,1,10,11,5,6,10,9,18,3,5
+YDR536W,Sce,S000002944,STL1,1,43,9,22,31,45,46,8,41,25,53,15,27,15,18,24,46,40,31,10,20
+YEL041W,Sce,S000000767,YEF1,1,23,10,35,33,23,23,9,36,31,42,11,27,20,11,27,45,34,37,5,13
+YEL057C,Sce,S000000783,,1,11,3,12,12,17,7,5,20,24,23,4,17,5,9,15,17,13,11,1,7
+YER015W,Sce,S000000817,FAA2,1,48,13,43,45,42,43,13,51,55,78,12,36,38,17,35,54,47,44,5,25
+YER024W,Sce,S000000826,YAT2,1,50,9,75,49,39,50,27,57,58,82,14,51,39,35,48,94,62,52,7,25
+YER065C,Sce,S000000867,ICL1,1,57,6,38,38,24,36,17,31,40,40,17,19,22,25,26,34,30,31,11,15
+YER103W,Sce,S000000905,SSA4,1,65,2,45,53,28,49,5,37,50,46,7,33,27,23,28,39,48,44,1,12
+YER121W,Sce,S000000923,,1,12,0,8,9,4,3,3,2,5,7,3,12,4,4,6,15,3,6,2,6
+YFL011W,Sce,S000001883,HXT10,1,32,12,14,21,41,53,2,50,23,41,18,15,20,15,25,45,35,48,13,23
+YFL030W,Sce,S000001864,AGX1,1,33,6,21,15,19,27,10,23,25,37,7,14,18,11,13,38,20,33,5,10
+YGL080W,Sce,S000003048,FMP37,1,10,1,4,7,9,7,2,7,15,12,3,4,6,6,3,7,11,5,2,9
+YGL117W,Sce,S000003085,,1,7,4,23,11,13,9,10,24,20,26,7,18,8,11,14,18,12,20,0,10
+YGL205W,Sce,S000003173,POX1,1,47,8,55,29,34,50,15,48,56,75,15,31,26,31,35,57,46,50,9,31
+YGL208W,Sce,S000003176,SIP2,1,17,4,32,27,10,21,8,21,27,26,10,18,32,24,22,44,34,23,3,12
+YGR043C,Sce,S000003275,NQM1,1,32,2,19,32,12,16,8,20,35,30,8,11,10,8,11,24,18,23,1,13
+YGR067C,Sce,S000003299,,1,27,14,44,33,54,17,22,65,50,88,16,56,31,38,26,103,38,47,12,23
+YGR201C,Sce,S000003433,,1,13,3,16,21,17,8,4,11,16,24,4,5,10,6,15,15,13,13,4,7
+YGR230W,Sce,S000003462,BNS1,1,6,3,7,3,6,3,5,5,18,12,2,11,5,9,11,14,8,7,0,2
+YGR236C,Sce,S000003468,SPG1,1,8,0,6,4,2,7,1,4,5,6,9,2,3,3,6,7,8,9,0,5
+YGR250C,Sce,S000003482,,1,28,5,50,54,36,40,20,49,49,46,17,75,40,42,26,82,34,36,7,45
+YGR256W,Sce,S000003488,GND2,1,51,6,32,25,21,46,11,40,32,43,11,18,20,13,24,28,23,25,8,15
+YHL032C,Sce,S000001024,GUT1,1,48,12,39,42,31,46,13,39,48,65,17,26,34,30,37,59,39,46,17,21
+YHR015W,Sce,S000001057,MIP6,1,24,10,26,46,39,25,11,44,73,55,11,63,17,29,29,61,39,34,4,19
+YHR096C,Sce,S000001138,HXT5,1,32,15,18,31,41,53,2,39,25,45,21,24,23,18,26,49,41,47,12,30
+YHR209W,Sce,S000001252,CRG1,1,15,5,16,23,17,12,4,22,20,23,5,18,14,6,15,27,12,15,7,15
+YIL107C,Sce,S000001369,PFK26,1,41,4,60,44,30,40,17,48,62,72,16,66,51,24,49,81,47,40,6,29
+YIL117C,Sce,S000001379,PRM5,1,11,0,15,16,9,15,6,20,18,28,6,19,20,9,12,59,26,18,2,9
+YIL136W,Sce,S000001398,OM45,1,42,0,28,43,9,26,2,13,49,27,5,19,6,23,25,34,10,12,10,10
+YIL155C,Sce,S000001417,GUT2,1,53,8,36,34,29,40,13,32,42,60,18,33,32,21,30,41,46,49,9,23
+YIL160C,Sce,S000001422,POT1,1,44,8,19,26,14,38,4,33,27,37,8,28,19,16,19,24,15,29,0,9
+YIR016W,Sce,S000001455,,1,21,5,27,15,6,15,9,12,9,21,5,4,13,10,20,43,11,13,2,4
+YIR038C,Sce,S000001477,GTT1,1,18,0,14,17,14,11,7,16,19,26,6,7,13,8,9,21,3,11,3,11
+YJL037W,Sce,S000003574,IRC18,1,12,4,4,17,8,15,1,18,21,26,5,11,1,8,8,17,19,23,1,5
+YJL045W,Sce,S000003581,,1,58,10,35,38,20,59,25,31,34,48,15,23,24,20,37,40,46,45,6,20
+YJL089W,Sce,S000003625,SIP4,1,16,15,58,33,57,17,14,48,64,125,7,100,28,34,20,88,43,25,11,26
+YJL137C,Sce,S000003673,GLG2,1,18,5,26,26,23,10,12,25,27,49,6,17,21,22,15,20,23,14,6,15
+YJL144W,Sce,S000003680,,1,0,1,6,6,2,10,4,5,2,6,2,13,3,5,9,14,7,5,0,4
+YJL153C,Sce,S000003689,INO1,1,31,6,34,32,20,31,9,32,40,56,11,39,25,19,17,35,29,42,4,21
+YJL161W,Sce,S000003697,FMP33,1,7,1,8,8,8,11,5,9,15,29,3,8,7,7,5,20,10,10,1,8
+YJL185C,Sce,S000003721,ATG36,1,13,4,21,25,17,7,7,16,8,27,2,19,15,9,24,43,13,11,4,8
+YJL191W,Sce,S000003727,RPS14B,1,18,1,9,4,3,15,2,6,9,7,3,3,5,4,15,8,11,13,0,2
+YJL216C,Sce,S000003752,IMA5,1,28,7,43,46,43,39,14,33,47,31,16,35,29,13,23,39,25,27,18,25
+YJL217W,Sce,S000003753,REE1,1,12,1,12,12,9,19,5,5,12,18,4,4,7,6,9,18,17,16,7,5
+YJR019C,Sce,S000003780,TES1,1,18,1,18,14,20,15,20,16,21,32,8,11,21,17,15,36,19,21,3,23
+YJR094C,Sce,S000003854,IME1,1,13,3,26,23,26,6,12,19,24,18,3,36,20,22,8,47,25,5,1,23
+YJR095W,Sce,S000003856,SFC1,1,28,3,5,18,12,28,7,25,28,27,8,13,17,13,14,17,21,24,1,13
+YJR096W,Sce,S000003857,,1,15,6,15,23,7,19,8,16,25,30,5,14,16,10,11,13,11,17,7,14
+YJR109C,Sce,S000003870,CPA2,1,91,11,65,82,45,66,16,84,75,102,19,57,47,33,41,83,62,87,8,44
+YJR156C,Sce,S000003917,THI11,1,24,10,20,23,13,22,5,22,34,33,8,10,18,14,11,15,17,17,4,20
+YKL026C,Sce,S000001509,GPX1,1,3,6,5,14,14,9,3,11,18,11,3,12,11,9,5,9,3,13,1,7
+YKL093W,Sce,S000001576,MBR1,1,19,12,19,20,14,15,5,11,18,25,6,28,23,13,18,58,22,8,0,5
+YKL107W,Sce,S000001590,,1,21,3,22,19,14,19,4,25,21,24,5,18,10,7,18,28,23,16,4,8
+YKL138C,Sce,S000001621,MRPL31,1,4,1,4,4,6,7,3,5,22,11,4,3,8,8,10,9,7,7,4,4
+YKL171W,Sce,S000001654,NNK1,1,42,10,55,43,40,45,26,49,59,85,20,61,52,38,51,136,50,32,9,25
+YKL187C,Sce,S000001670,FAT3,1,66,4,39,23,26,31,10,56,23,103,13,55,29,29,18,86,76,37,6,20
+YKR009C,Sce,S000001717,FOX2,1,79,6,39,51,45,72,18,56,77,77,12,49,39,28,28,58,56,71,10,29
+YKR049C,Sce,S000001757,FMP46,1,4,3,10,4,5,5,2,8,12,13,3,6,8,12,8,8,7,7,5,3
+YKR067W,Sce,S000001775,GPT2,1,47,8,36,37,39,34,16,57,61,72,10,32,41,19,41,68,39,55,4,27
+YKR075C,Sce,S000001783,,1,8,5,23,23,9,4,21,23,20,25,8,27,7,12,14,34,17,12,5,10
+YKR076W,Sce,S000001784,ECM4,1,19,3,29,23,20,17,14,23,28,27,3,15,14,12,20,27,23,23,10,20
+YKR091W,Sce,S000001799,SRL3,1,16,2,11,18,9,3,7,9,18,19,4,15,22,7,13,35,19,13,2,4
+YLR174W,Sce,S000004164,IDP2,1,28,1,29,31,16,28,9,33,34,30,12,10,14,13,19,22,31,30,5,17
+YLR194C,Sce,S000004184,,1,23,1,6,10,3,16,1,7,12,12,2,11,6,9,0,52,52,21,4,6
+YLR284C,Sce,S000004274,ECI1,1,17,6,13,18,17,18,4,18,23,30,6,22,10,6,11,21,10,15,2,13
+YLR307W,Sce,S000004298,CDA1,1,15,7,23,21,17,17,6,26,14,27,5,14,16,11,13,12,24,14,8,11
+YLR377C,Sce,S000004369,FBP1,1,23,5,24,16,20,30,8,25,18,34,7,19,15,11,15,24,21,22,2,9
+YLR411W,Sce,S000004403,CTR3,1,12,11,12,12,13,16,2,19,16,24,6,7,7,7,10,21,13,13,7,13
+YML042W,Sce,S000004506,CAT2,1,32,7,39,36,37,31,20,38,54,61,18,44,35,34,25,56,33,30,11,29
+YML054C,Sce,S000004518,CYB2,1,45,8,36,39,15,38,9,34,55,59,10,27,34,19,26,36,30,46,6,19
+YML122C,Sce,S000004591,,1,11,8,2,5,6,5,3,6,4,10,3,7,4,5,14,15,6,4,2,6
+YML128C,Sce,S000004597,MSC1,1,22,0,54,19,22,17,7,17,62,48,7,33,11,26,11,60,27,28,21,21
+YMR006C,Sce,S000004608,PLB2,1,57,10,44,25,29,53,4,37,24,64,14,61,27,14,18,97,64,30,11,23
+YMR011W,Sce,S000004613,HXT2,1,36,11,14,24,43,53,2,48,24,37,20,19,17,15,20,44,35,45,10,24
+YMR095C,Sce,S000004701,SNO1,1,17,6,11,12,13,13,8,15,13,21,4,11,10,9,9,14,14,18,2,4
+YMR096W,Sce,S000004702,SNZ1,1,30,5,18,25,8,25,6,22,24,21,13,6,11,6,11,22,11,30,2,1
+YMR107W,Sce,S000004713,SPG4,1,4,0,9,9,4,8,3,3,8,5,4,8,5,7,9,13,3,8,1,4
+YMR118C,Sce,S000004724,SHH3,1,10,0,5,8,11,15,7,12,11,21,7,7,7,5,10,18,14,14,6,8
+YMR174C,Sce,S000004786,PAI3,1,5,0,7,6,2,4,2,1,13,2,2,3,0,7,0,6,3,3,0,2
+YMR175W,Sce,S000004787,SIP18,1,4,0,8,4,1,10,3,1,11,1,11,9,0,4,2,6,2,0,1,1
+YMR191W,Sce,S000004803,SPG5,1,21,3,14,15,23,17,8,22,19,33,9,29,16,11,21,46,24,23,6,13
+YMR280C,Sce,S000004893,CAT8,1,75,16,83,60,60,59,26,71,107,159,37,143,70,63,63,150,98,54,5,34
+YMR303C,Sce,S000004918,ADH2,1,37,8,15,21,8,42,11,22,24,25,5,13,15,6,8,24,14,32,5,13
+YNL009W,Sce,S000004954,IDP3,1,24,2,31,24,21,27,7,36,47,35,15,18,12,15,19,22,29,20,4,12
+YNL012W,Sce,S000004957,SPO1,1,21,11,33,41,45,34,9,48,61,63,13,43,28,16,18,54,30,32,5,26
+YNL194C,Sce,S000005138,,1,23,6,6,8,22,16,5,15,13,27,6,18,13,9,18,26,27,22,7,14
+YNL195C,Sce,S000005139,,1,19,4,18,12,3,20,11,9,12,9,9,23,18,13,12,31,15,13,1,9
+YNL202W,Sce,S000005146,SPS19,1,36,5,14,14,15,29,4,16,27,27,3,12,8,7,9,15,17,25,2,7
+YNL270C,Sce,S000005214,ALP1,1,43,7,18,28,45,44,3,54,24,54,12,18,24,18,24,51,26,44,16,20
+YNL335W,Sce,S000005279,DDI3,1,18,3,14,11,9,12,6,14,7,19,3,12,11,8,13,13,20,20,3,9
+YNR002C,Sce,S000005285,ATO2,1,29,4,9,12,28,30,3,19,9,29,6,16,10,7,7,19,15,15,5,10
+YNR056C,Sce,S000005339,BIO5,1,29,19,15,20,48,35,10,56,20,49,16,22,22,11,15,63,32,49,10,20
+YNR058W,Sce,S000005341,BIO3,1,25,12,25,28,19,32,18,33,33,41,14,23,23,22,10,35,22,41,7,17
+YNR060W,Sce,S000005343,FRE4,1,58,12,18,37,44,44,22,50,45,75,16,32,28,17,33,44,42,45,10,47
+YOL083W,Sce,S000005443,ATG34,1,11,7,19,36,29,22,6,32,37,34,7,27,20,19,8,40,23,23,3,9
+YOL101C,Sce,S000005461,IZH4,1,10,5,8,17,33,7,9,27,20,41,6,18,7,9,7,27,24,18,3,16
+YOL126C,Sce,S000005486,MDH2,1,24,5,20,14,9,28,11,33,17,38,9,24,20,16,14,37,14,34,0,10
+YOL147C,Sce,S000005507,PEX11,1,22,3,12,5,13,10,5,8,17,35,4,11,4,13,14,16,10,21,5,8
+YOR100C,Sce,S000005626,CRC1,1,28,3,7,12,18,34,3,21,26,28,7,15,16,12,10,31,24,23,2,7
+YOR120W,Sce,S000005646,GCY1,1,20,2,18,19,8,16,9,22,28,30,3,19,19,13,10,18,19,24,7,8
+YOR180C,Sce,S000005706,DCI1,1,15,4,9,14,19,16,7,18,23,33,5,18,9,10,4,25,14,21,1,6
+YOR388C,Sce,S000005915,FDH1,1,32,4,24,28,8,30,9,25,29,29,6,22,12,13,18,17,18,33,3,16
+YPL036W,Sce,S000005957,PMA2,1,103,9,53,61,37,76,13,69,46,89,22,31,34,26,34,71,56,79,15,23
+YPL109C,Sce,S000006030,,1,27,9,39,40,43,27,15,57,49,79,15,32,23,25,36,49,30,35,9,18
+YPL113C,Sce,S000006034,,1,19,9,25,25,18,24,9,28,34,34,8,20,14,8,15,27,23,32,7,17
+YPL134C,Sce,S000006055,ODC1,1,25,2,9,12,19,26,4,19,27,28,8,11,16,10,13,16,20,31,3,11
+YPL147W,Sce,S000006068,PXA1,1,43,6,49,39,49,43,14,77,65,107,19,54,29,25,54,63,41,50,9,34
+YPL156C,Sce,S000006077,PRM4,1,13,1,15,23,14,6,5,20,26,36,2,19,12,8,10,37,17,14,1,5
+YPL186C,Sce,S000006107,UIP4,1,15,0,27,42,13,19,7,9,27,13,4,27,14,9,5,25,23,14,5,6
+YPL201C,Sce,S000006122,YIG1,1,9,5,34,18,28,28,15,32,27,51,6,42,14,24,13,38,25,25,3,24
+YPL230W,Sce,S000006151,USV1,1,20,4,13,12,15,11,15,19,24,13,8,40,31,21,20,68,30,12,0,15
+YPL276W,Sce,S000006197,,1,10,2,6,17,3,11,4,11,8,13,2,8,5,3,6,6,11,15,0,4
+YPR001W,Sce,S000006205,CIT3,1,28,7,16,27,19,40,13,32,28,63,16,29,24,17,21,41,26,21,6,12
+YPR002W,Sce,S000006206,PDH1,1,46,6,31,23,22,30,14,35,44,51,12,27,20,19,22,29,28,35,5,17
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 729
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