Commit e095e5eb authored by mcariou's avatar mcariou
Browse files

update doc

parent aff74e46
......@@ -331,7 +331,7 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
<<>>=
library(ape)
aln<-paste0(home, "fasta/78Lp/")
aln<-paste0(home, "fasta/78Lp_V2/")
subrep<-list.files(aln)
subrep<-subrep[grep(x=subrep, pattern="Q5")]
subrep
......@@ -348,8 +348,10 @@ file<-list.files(paste0(aln, "/", subrepcurrent))
file<-file[grep(x=file, pattern="aln")]
if (length(file)>0){
fasta<-read.dna(paste0(aln, "/",subrepcurrent, "/", file), format="fasta", as.character=TRUE)
rownames(fasta)<-sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1])
cat<-c(cat, rownames(fasta))
tmprownames<-ifelse(grepl(rownames(fasta), pattern = "pneumo"),
substr(rownames(fasta)[grep(pattern = "pneumophila",rownames(fasta))], 1,31),
sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1]))
cat<-c(cat, tmprownames)
}
}
......@@ -364,14 +366,17 @@ colnames(tab)<-subrep
# make a cat list containing all species names
for (subrepcurrent in subrep){
print(subrepcurrent)
#print(subrepcurrent)
file<-list.files(paste0(aln, "/", subrepcurrent))
file<-file[grep(x=file, pattern="aln")]
if (length(file)>0){
fasta<-read.dna(paste0(aln, "/",subrepcurrent, "/", file), format="fasta", as.character=TRUE)
rownames(fasta)<-sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1])
tmp<-ifelse(rownames(tab) %in% rownames(fasta), 1, 0)
tmprownames<-ifelse(grepl(rownames(fasta), pattern = "pneumo"),
substr(rownames(fasta)[grep(pattern = "pneumophila",rownames(fasta))], 1,31),
sapply(rownames(fasta), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1]))
tmp<-ifelse(rownames(tab) %in% tmprownames, 1, 0)
tab[,subrepcurrent]<-tmp
}
}
......@@ -397,7 +402,7 @@ barplot(vectgene, horiz=TRUE, las=2)
\subsection{Concatenate and Supertree}
<<tree, fig.height=12>>=
treepath<-paste0(home, "fasta/78Lp/cat.phylip_phyml_tree")
treepath<-paste0(home, "fasta/78Lp_V2/cat.phylip_phyml_tree")
tree<-read.tree(treepath)
plot(root(tree, outgroup = "Coxiella_burnetii"))
......
......@@ -20,11 +20,11 @@
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Objective}{2}{subsection.1.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Data}{2}{subsection.1.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.1}Data from the first publication:}{2}{subsubsection.1.2.1}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{5}{subsubsection.1.2.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{13}{subsubsection.1.2.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Add missing species}{14}{subsection.1.3}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Get genes sequences}{15}{section.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{15}{subsection.2.1}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Phylogeny}{16}{section.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genes alignement}{16}{subsection.3.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{26}{subsection.3.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{4}{subsubsection.1.2.2}}
\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{10}{subsubsection.1.2.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Add missing species}{11}{subsection.1.3}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Get genes sequences}{12}{section.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}}
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......@@ -2,11 +2,11 @@
\contentsline {subsection}{\numberline {1.1}Objective}{2}{subsection.1.1}
\contentsline {subsection}{\numberline {1.2}Data}{2}{subsection.1.2}
\contentsline {subsubsection}{\numberline {1.2.1}Data from the first publication:}{2}{subsubsection.1.2.1}
\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{5}{subsubsection.1.2.2}
\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{13}{subsubsection.1.2.3}
\contentsline {subsection}{\numberline {1.3}Add missing species}{14}{subsection.1.3}
\contentsline {section}{\numberline {2}Get genes sequences}{15}{section.2}
\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{15}{subsection.2.1}
\contentsline {section}{\numberline {3}Phylogeny}{16}{section.3}
\contentsline {subsection}{\numberline {3.1}Genes alignement}{16}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{26}{subsection.3.2}
\contentsline {subsubsection}{\numberline {1.2.2}Data from the seconde publication:}{4}{subsubsection.1.2.2}
\contentsline {subsubsection}{\numberline {1.2.3}Data from Legionella pneumophila reference strains:}{10}{subsubsection.1.2.3}
\contentsline {subsection}{\numberline {1.3}Add missing species}{11}{subsection.1.3}
\contentsline {section}{\numberline {2}Get genes sequences}{12}{section.2}
\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}
\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}
\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}
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......@@ -64,7 +64,6 @@ GCA_900461525.1;Legionella busanensis;Pillon
GCA_000236145.1;Legionella dumoffi;Pillon
GCA_003990055.1;Legionella septentrionalis;Pillon
GCA_900452385.1;Legionella donaldsonii;Pillon
GCA_001648685.1;Legionella gormannii;Pillon
GCA_001886835.1;Legionella fraseri Dallas1E;Pillon
GCA_003003865.1;Legionella fraseri Lansing 3;Pillon
GCA_003003755.1;Legionella fraseri Los Angeles 1;Pillon
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