continue doc

3b0f558d · mcariou · 59d4b779 · 3b0f558d · 3b0f558d · 3b0f558d
Commit 3b0f558d authored Oct 04, 2021 by mcariou
--- 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}



--- a/doc/1_reference_legio_phylo.log
+++ b/doc/1_reference_legio_phylo.log
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+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
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 []


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+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
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@@ -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
 []


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+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)))[][] 
 []


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+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]

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+
+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[] []=[] []""[][])[][] 
 []


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+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"[][])[][] 
 []


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+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[] []=[] []""[][])[][] 
 []

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+(/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
+ []
+
+
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--- a/doc/1_reference_legio_phylo.pdf
+++ b/doc/1_reference_legio_phylo.pdf
--- 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}