diff --git a/doc/1_reference_legio_phylo.Rnw b/doc/1_reference_legio_phylo.Rnw
index effc056040d58ff7d4ebefa6bbf59443925fd99b..c9edac49297779c180db4a13011a914d0961488e 100644
--- a/doc/1_reference_legio_phylo.Rnw
+++ b/doc/1_reference_legio_phylo.Rnw
@@ -80,10 +80,15 @@ tabPRJNA<-read.table(paste0(data, "PRJNA285910_AssemblyDetails.txt"), header=FAL
tabPRJNA<-tabPRJNA[,1:6]
names(tabPRJNA)<-c("Assembly", "Level", "WGS", "BioSample", "Strain", "Taxonomy")
+
+tabAss<-tabPRJNA[, c("Assembly","Taxonomy")]
+tabAss$Origin<-"Burstein"
+
+
@
-
+Data from the seconde publication:
\url{https://pubmed.ncbi.nlm.nih.gov/33881638/}
@@ -136,6 +141,55 @@ ncbi2<-read.table(paste0(data, "tab_ncbi_contigs_parsed.csv"), sep=";", fill=TRU
@
+
+Data from Legionella pneumophila reference strains:
+\begin{itemize}
+ \item Legionella pneumophila Paris complete genome : CR628336.1 - GCA\_000048645.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/CR628336)
+
+ \item Legionella pneumophila Lens complete genome : CR628337.1 - GCA\_000048665.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/CR628337)
+
+ \item Legionella pneumophila Philadelphia complete genome : NC\_002942 - GCA\_000008485.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/52840256)
+
+ \item Legionella pneumophila Corby complete genome : NC\_009494 - GCA\_000092545.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/NC\_009494.2)
+ \item Legionella pneumophila Alcoy complete genome : NC\_014125 - GCA\_000092625.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/NC\_014125.1)
+
+ \item Optionnel : Legionella pneumophila Lorraine complete genome : FQ958210.1 - GCA\_000306865.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/FQ958210.1)
+\end{itemize}
+
+<<>>=
+Taxonomy<-c("Legionella pneumophila Paris",
+ "Legionella pneumophila Lens",
+ "Legionella pneumophila Philadelphia",
+ "Legionella pneumophila Corby",
+ "Legionella pneumophila Alcoy",
+ "Legionella pneumophila Lorraine")
+
+Assembly<-c("GCA_000048645.1", "GCA_000048665.1",
+ "GCA_000008485.1", "GCA_000092545.1",
+ "GCA_000092625.1", "GCA_000306865.1")
+
+
+Origin<-rep("pneumo", 6)
+
+tabAss<-rbind(tabAss, cbind(Taxonomy, Assembly, Origin))
+
+@
+
+
+
+
\section{Get genes sequences}
diff --git a/doc/1_reference_legio_phylo.log b/doc/1_reference_legio_phylo.log
index 93091f66c8c67d9d2ed1fc1755cd8d488617211b..2715b2247797331de96b21d98c7d8445a8a76a1e 100644
--- a/doc/1_reference_legio_phylo.log
+++ b/doc/1_reference_legio_phylo.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.6.16) 20 SEP 2021 16:35
+This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.6.16) 4 OCT 2021 16:53
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
@@ -881,10 +881,10 @@ Overfull \hbox (209.12009pt too wide) in paragraph at lines 158--158
[]
-Package xcolor Warning: Incompatible color definition on input line 170.
+Package xcolor Warning: Incompatible color definition on input line 173.
-Overfull \hbox (208.8464pt too wide) in paragraph at lines 176--176
+Overfull \hbox (208.8464pt too wide) in paragraph at lines 179--179
[][]\OT1/cmtt/m/n/10.95 gupta1[][]<-[][]read.table[][]([][]paste0[][](data, dat
alist2[[][]1[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char
@@ -892,7 +892,7 @@ alist2[[][]1[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
[]
-Overfull \hbox (208.8464pt too wide) in paragraph at lines 180--180
+Overfull \hbox (208.8464pt too wide) in paragraph at lines 183--183
[][]\OT1/cmtt/m/n/10.95 gupta2[][]<-[][]read.table[][]([][]paste0[][](data, dat
alist2[[][]2[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char
@@ -900,76 +900,116 @@ alist2[[][]2[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t
[]
-Package xcolor Warning: Incompatible color definition on input line 192.
+Package xcolor Warning: Incompatible color definition on input line 195.
-Overfull \hbox (30.91077pt too wide) in paragraph at lines 198--198
+Overfull \hbox (30.91077pt too wide) in paragraph at lines 201--201
[] []\OT1/cmtt/m/n/10.95 is.there[][]<-[][]sum[][]([][]sapply[][](species,[]
[]function[][]([][]y[][])[] []grepl[][](x,[][]pattern[] []= y)))[][]
[]
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 210--210
+Overfull \hbox (128.63846pt too wide) in paragraph at lines 213--213
[][]\OT1/cmtt/m/n/10.95 list[][]<-[][]c[][](list[[][]grep[][](list,[] []pattern
[][]=[][]"Legionella"[][])], list[[][]grep[][](list,[] []pattern[][]=[][]"Coxie
lla"[][])])[][]
[]
+[3]
-Package xcolor Warning: Incompatible color definition on input line 217.
+Package xcolor Warning: Incompatible color definition on input line 220.
-[3]
-Overfull \hbox (232.11484pt too wide) in paragraph at lines 219--219
+
+Overfull \hbox (232.11484pt too wide) in paragraph at lines 222--222
[][]\OT1/cmtt/m/n/10.95 ncbi[][]<-[][]read.table[][]([][]paste0[][](data,[] []"
tab_ncbi_file.csv"[][]),[] []sep[][]=[][]";"[][],[] []fill[][]=[][]TRUE[][],[]
[]header[][]=[][]TRUE[][],[] []comment.char[] []=[] []""[][])[][]
[]
-Overfull \hbox (7.91602pt too wide) in paragraph at lines 220--220
+Overfull \hbox (7.91602pt too wide) in paragraph at lines 223--223
[][]\OT1/cmtt/m/n/10.95 sp[][]<-[][]c[][]([][]"adelaidensis"[][],[] []"birmingh
amensis"[][],[] []"brunensis"[][],[] []"cherrii"[][])[][]
[]
-Overfull \hbox (295.3504pt too wide) in paragraph at lines 221--221
+Overfull \hbox (295.3504pt too wide) in paragraph at lines 224--224
[][]\OT1/cmtt/m/n/10.95 ncbi2[][]<-[][]read.table[][]([][]paste0[][](data,[] []
"tab_ncbi_contigs_parsed.csv"[][]),[] []sep[][]=[][]";"[][],[] []fill[][]=[][]T
RUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char[] []=[] []""[][])[][]
[]
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 246.
+LaTeX Font Info: Try loading font information for TS1+cmr on input line 232.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd
+File: ts1cmr.fd 2014/09/29 v2.5h Standard LaTeX font definitions
+)
+Overfull \hbox (51.54103pt too wide) in paragraph at lines 232--233
+[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Paris com-plete genome : CR628336.
+1 - GCA[]000048645.1
+ []
+
+
+Overfull \hbox (49.38147pt too wide) in paragraph at lines 236--237
+[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Lens com-plete genome : CR628337.1
+ - GCA[]000048665.1
+ []
+
+
+Overfull \hbox (52.07639pt too wide) in paragraph at lines 244--245
+[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Corby com-plete genome : NC[]00949
+4 - GCA[]000092545.1
+ []
+
+
+Overfull \hbox (49.9168pt too wide) in paragraph at lines 247--248
+[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Al-coy com-plete genome : NC[]0141
+25 - GCA[]000092625.1
+ []
+
+
+Overfull \hbox (29.24263pt too wide) in paragraph at lines 251--252
+[]\OT1/cmr/m/n/10.95 Optionnel : Le-gionella pneu-mophila Lor-raine com-plete g
+enome : FQ958210.1
+ []
+
+
+Package xcolor Warning: Incompatible color definition on input line 257.
+
[4]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 246.
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 301.
+[5]
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 301.
(./1_reference_legio_phylo.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 246.
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+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 301.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 301.
Package rerunfilecheck Info: File `1_reference_legio_phylo.out' has not changed
.
(rerunfilecheck) Checksum: C7F3B916942DAC9C7581F4EFD94AC3C7;701.
-Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 246.
+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 301.
)
Here is how much of TeX's memory you used:
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+Output written on 1_reference_legio_phylo.pdf (5 pages, 127639 bytes).
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diff --git a/doc/1_reference_legio_phylo.pdf b/doc/1_reference_legio_phylo.pdf
index ca5c11ebcefdd893edfe2a8611fb73fe566695cf..aa180512d7fd1fac5703b92975d78b8f89898be4 100644
Binary files a/doc/1_reference_legio_phylo.pdf and b/doc/1_reference_legio_phylo.pdf differ
diff --git a/doc/1_reference_legio_phylo.tex b/doc/1_reference_legio_phylo.tex
index 4d19f7ec8eb94635c78912de479ccaeb8ee23a21..1a7dad090814000ef4354bd2fc28209bfc576d40 100644
--- a/doc/1_reference_legio_phylo.tex
+++ b/doc/1_reference_legio_phylo.tex
@@ -156,12 +156,15 @@ Data from the first publication:
\hlstd{tabPRJNA}\hlkwb{<-}\hlstd{tabPRJNA[,}\hlnum{1}\hlopt{:}\hlnum{6}\hlstd{]}
\hlkwd{names}\hlstd{(tabPRJNA)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Assembly"}\hlstd{,} \hlstr{"Level"}\hlstd{,} \hlstr{"WGS"}\hlstd{,} \hlstr{"BioSample"}\hlstd{,} \hlstr{"Strain"}\hlstd{,} \hlstr{"Taxonomy"}\hlstd{)}
+
+\hlstd{tabAss}\hlkwb{<-}\hlstd{tabPRJNA[,} \hlkwd{c}\hlstd{(}\hlstr{"Assembly"}\hlstd{,}\hlstr{"Taxonomy"}\hlstd{)]}
+\hlstd{tabAss}\hlopt{$}\hlstd{Origin}\hlkwb{<-}\hlstr{"Burstein"}
\end{alltt}
\end{kframe}
\end{knitrout}
-
+Data from the seconde publication:
\url{https://pubmed.ncbi.nlm.nih.gov/33881638/}
@@ -223,6 +226,58 @@ Which species are present in gupta not in the previous datasets.
\end{kframe}
\end{knitrout}
+
+Data from Legionella pneumophila reference strains:
+\begin{itemize}
+ \item Legionella pneumophila Paris complete genome : CR628336.1 - GCA\_000048645.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/CR628336)
+
+ \item Legionella pneumophila Lens complete genome : CR628337.1 - GCA\_000048665.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/CR628337)
+
+ \item Legionella pneumophila Philadelphia complete genome : NC\_002942 - GCA\_000008485.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/52840256)
+
+ \item Legionella pneumophila Corby complete genome : NC\_009494 - GCA\_000092545.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/NC\_009494.2)
+ \item Legionella pneumophila Alcoy complete genome : NC\_014125 - GCA\_000092625.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/NC\_014125.1)
+
+ \item Optionnel : Legionella pneumophila Lorraine complete genome : FQ958210.1 - GCA\_000306865.1
+
+ (https://www.ncbi.nlm.nih.gov/nuccore/FQ958210.1)
+\end{itemize}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{Taxonomy}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Legionella pneumophila Paris"}\hlstd{,}
+ \hlstr{"Legionella pneumophila Lens"}\hlstd{,}
+ \hlstr{"Legionella pneumophila Philadelphia"}\hlstd{,}
+ \hlstr{"Legionella pneumophila Corby"}\hlstd{,}
+ \hlstr{"Legionella pneumophila Alcoy"}\hlstd{,}
+ \hlstr{"Legionella pneumophila Lorraine"}\hlstd{)}
+
+\hlstd{Assembly}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"GCA_000048645.1"}\hlstd{,} \hlstr{"GCA_000048665.1"}\hlstd{,}
+ \hlstr{"GCA_000008485.1"}\hlstd{,} \hlstr{"GCA_000092545.1"}\hlstd{,}
+ \hlstr{"GCA_000092625.1"}\hlstd{,} \hlstr{"GCA_000306865.1"}\hlstd{)}
+
+
+\hlstd{Origin}\hlkwb{<-}\hlkwd{rep}\hlstd{(}\hlstr{"pneumo"}\hlstd{,} \hlnum{6}\hlstd{)}
+
+\hlstd{tabAss}\hlkwb{<-}\hlkwd{rbind}\hlstd{(tabAss,} \hlkwd{cbind}\hlstd{(Taxonomy, Assembly, Origin))}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+
\section{Get genes sequences}