Commit 3b0f558d authored by mcariou's avatar mcariou
Browse files

continue doc

parent 59d4b779
......@@ -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}
......
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[][]\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
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[]
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[][]\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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[] []\OT1/cmtt/m/n/10.95 is.there[][]<-[][]sum[][]([][]sapply[][](species,[]
[]function[][]([][]y[][])[] []grepl[][](x,[][]pattern[] []= y)))[][]
[]
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[][]\OT1/cmtt/m/n/10.95 list[][]<-[][]c[][](list[[][]grep[][](list,[] []pattern
[][]=[][]"Legionella"[][])], list[[][]grep[][](list,[] []pattern[][]=[][]"Coxie
lla"[][])])[][]
[]
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[][]\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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[][]\OT1/cmtt/m/n/10.95 sp[][]<-[][]c[][]([][]"adelaidensis"[][],[] []"birmingh
amensis"[][],[] []"brunensis"[][],[] []"cherrii"[][])[][]
[]
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[][]\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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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Paris com-plete genome : CR628336.
1 - GCA[]000048645.1
[]
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Lens com-plete genome : CR628337.1
- GCA[]000048665.1
[]
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Corby com-plete genome : NC[]00949
4 - GCA[]000092545.1
[]
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[]\OT1/cmr/m/n/10.95 Legionella pneu-mophila Al-coy com-plete genome : NC[]0141
25 - GCA[]000092625.1
[]
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[]\OT1/cmr/m/n/10.95 Optionnel : Le-gionella pneu-mophila Lor-raine com-plete g
enome : FQ958210.1
[]
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......@@ -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}
......
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