diff --git a/doc/1_reference_legio_phylo.Rnw b/doc/1_reference_legio_phylo.Rnw index 9b7a32f7340f1cd73e760239192805dda8f4cf6e..c8907eb193c6c47b68feae50600ec2e89e2f3ad1 100644 --- a/doc/1_reference_legio_phylo.Rnw +++ b/doc/1_reference_legio_phylo.Rnw @@ -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")) diff --git a/doc/1_reference_legio_phylo.aux b/doc/1_reference_legio_phylo.aux index 05788fefe4c078076c22c2c073cda4a54447470f..16fa2758ad7b946bc505e87cffafad514759911b 100644 --- a/doc/1_reference_legio_phylo.aux +++ b/doc/1_reference_legio_phylo.aux @@ -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}} diff --git a/doc/1_reference_legio_phylo.log b/doc/1_reference_legio_phylo.log index 078f7758357f42ceaa235044e647bac4849f4dda..78c41e7d2344f44406333f6c021fc2e226591504 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 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(/usr/share/texmf/tex/latex/R/tex/latex/omscmtt.fd File: omscmtt.fd ) LaTeX Font Info: Font shape `OMS/cmtt/m/n' in size <10.95> not available -(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 148. +(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 140. -Overfull \hbox (243.33853pt too wide) in paragraph at lines 148--148 +Overfull \hbox (243.33853pt too wide) in paragraph at lines 140--140 [][]\OT1/cmtt/m/n/10.95 tab1[][]<-[][]read.table[][]([][]paste0[][](data, datal ist1[[][]1[][]]),[] []skip[][]=[][]2[][],[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE @@ -786,10 +833,53 @@ n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE [] -Package xcolor Warning: Incompatible color definition on input line 178. +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## Species ATCC.number Strain.designation + Isolation ORF.prefix[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 1 L. adelaidensis ATCC49625 ATCC49625 Wa +ter in cooling tower (Adelaide, Australia) Lade[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 2 L. anisa ATCC35292 WA-316-C3 + Tap water (Los Angeles, CA, USA) Lani[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 + Lung biopsy (Alabama, USA) Lbir[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 4 L. bozemanii ATCC33217 WIGA + Lung tissue (Key West, FL, USA) Lboz[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 5 L. brunensis ATCC43878 ATCC43878 + Cooling tower water (Czechoslovakia) Lbru[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158 +[]\OT1/cmtt/m/n/10.95 ## 6 L. cherrii ATCC35252 ORW + Thermally altered water (Minnesota, USA) Lche[] + [] + +[2] +Package xcolor Warning: Incompatible color definition on input line 163. -Overfull \hbox (392.80441pt too wide) in paragraph at lines 180--180 + +Overfull \hbox (392.80441pt too wide) in paragraph at lines 165--165 [][]\OT1/cmtt/m/n/10.95 tabPRJNA[][]<-[][]read.table[][]([][]paste0[][](data,[] []"PRJNA285910_AssemblyDetails.txt"[][]),[] []header[][]=[][]FALSE[][],[] []se p[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t"[][],[] []skip[][]=[][]2[ @@ -797,27 +887,99 @@ p[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t"[][],[] []skip[][]=[][]2[ [] -Overfull \hbox (209.12009pt too wide) in paragraph at lines 183--183 +Overfull \hbox (209.12009pt too wide) in paragraph at lines 168--168 [][]\OT1/cmtt/m/n/10.95 names[][](tabPRJNA)[][]<-[][]c[][]([][]"Assembly"[][],[ ] []"Level"[][],[] []"WGS"[][],[] []"BioSample"[][],[] []"Strain"[] [],[] []"Taxonomy"[][])[][] [] -Overfull \hbox (7.91602pt too wide) in paragraph at lines 241--241 -[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m -icdadei[] +Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [1] Fluoribacter dumoffii NY 23 Fluoribacter go +rmanii Legionella adelaidensis[] + [] + + +Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [4] Legionella anisa Legionella birm +inghamensis Legionella bozemanae[] + [] + + +Overfull \hbox (226.36615pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [7] Legionella brunensis Legionella cher +rii Legionella cincinnatiensis[] + [] + + +Overfull \hbox (180.37665pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [10] Legionella drozanskii LLAP-1 Legionella eryt +hra Legionella feeleii[] [] -[3] [4] -Package xcolor Warning: Incompatible color definition on input line 247. +Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [13] Legionella geestiana Legionella grat +iana Legionella hackeliae[] + [] -Package xcolor Warning: Incompatible color definition on input line 259. +Overfull \hbox (186.12534pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [16] Legionella israelensis Legionella jame +stowniensis Legionella jordanis[] + [] -Overfull \hbox (208.8464pt too wide) in paragraph at lines 269--269 +Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [19] Legionella lansingensis Legionella lond +iniensis Legionella maceachernii[] + [] + + +Overfull \hbox (209.12009pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [22] Legionella moravica Legionella naut +arum Legionella oakridgensis[] + [] + + +Overfull \hbox (203.3714pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [25] Legionella parisiensis Legionella quat +eirensis Legionella quinlivanii[] + [] + + +Overfull \hbox (203.3714pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [28] Legionella rubrilucens Legionella sain +thelensi Legionella santicrucis[] + [] + + +Overfull \hbox (180.37665pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [31] Legionella shakespearei DSM 23087 Legionella spir +itensis Legionella steelei[] + [] + + +Overfull \hbox (191.87402pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## [34] Legionella steigerwaltii Legionella tucs +onensis Legionella waltersii[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 201--201 +[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go +rmanii Legionella adelaidensis ... Tatlockia micdadei[] + [] + +[3] + +Package xcolor Warning: Incompatible color definition on input line 207. + + +Package xcolor Warning: Incompatible color definition on input line 219. + + +Overfull \hbox (208.8464pt too wide) in paragraph at lines 229--229 [][]\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 @@ -825,181 +987,505 @@ alist2[[][]1[][]]),[] []sep[][]=[][]"\OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/n/10.95 t [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## - Type.Strain[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## Species + Type.Strain[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 1 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 1 -03645; DSM 19888; NCTC 12735[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 1 Legionella adelaidensis 1762-Aus-E; ATCC + 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 2 ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM - 7573; NCTC 11974; WA-316-C3[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 2 Legionella anisa ATCC 35292; CCUG 29665; + CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 3 ATCC 700512; CIP 106632; DSM 19152; Montb\xe -9liard A1; Montb\xe9liard A1[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 3 Legionella beliardensis ATCC 700512; CIP +106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 4 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM - 19232; JCM 7559; NCTC 12437[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 4 Legionella birminghamensis 1407-AL-H; ATCC 43702; CC +UG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 5 ALLO1; ATCC 33217; - CIP 103872; DSM 16523; WIGA[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 5 Legionella bozemanae + ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA[] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 302--302 -[]\OT1/cmtt/m/n/10.95 ## 6 441-1; ATCC 43878; CCUG 31114; CIP 1 -03874; DSM 19236; NCTC 12240[] +Overfull \hbox (283.85303pt too wide) in paragraph at lines 255--255 +[]\OT1/cmtt/m/n/10.95 ## 6 Legionella brunensis 441-1; AT +CC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## Type.Strain.chosen Type_Strain_Availability Number_o f_Assemblies[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 1 1762-Aus-E Y 3[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 2 <NA> N 5[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 3 <NA> N 2[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 4 1407-AL-H Y 3[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 5 WIGA Y 5[] [] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 302--302 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 6 ATCC 43878 Y 2[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## Available_Genome_Accession_Number_.Ref_Seq_is_provid ed_when_available.[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 1 NZ _CAAAHS000000000.1[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 2 NZ_CP029563.1[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 3 NZ_UGNV01000001.1[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 4 NZ_LNXT00000000.1[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 5 NZ_LNXU01000019.1[] [] -Overfull \hbox (71.15158pt too wide) in paragraph at lines 302--302 +Overfull \hbox (71.15158pt too wide) in paragraph at lines 255--255 []\OT1/cmtt/m/n/10.95 ## 6 NZ_LNXV01000029.1[] [] LaTeX Font Info: Font shape `OMS/cmtt/m/it' in size <10.95> not available -(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 304. +(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 257. -Overfull \hbox (216.49614pt too wide) in paragraph at lines 304--304 +Overfull \hbox (216.49614pt too wide) in paragraph at lines 257--257 [][]\OT1/cmtt/m/it/10.95 #gupta2<-read.table(paste0(data, datalist2[2]), sep="\ OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 t", fill=TRUE, header=TRUE, comment.ch ar = "")[][] [] -[5] +[4] -Package xcolor Warning: Incompatible color definition on input line 314. +Package xcolor Warning: Incompatible color definition on input line 267. -Overfull \hbox (7.91602pt too wide) in paragraph at lines 358--358 -[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m -icdadei[] +Overfull \hbox (226.36615pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [1] Legionella adelaidensis Legionella anis +a Legionella birminghamensis[] [] -Overfull \hbox (7.91602pt too wide) in paragraph at lines 444--444 -[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia m -icdadei[] +Overfull \hbox (180.37665pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [4] Legionella bozemanae Legionella brun +ensis Legionella cherrii[] [] -[6] [7] [8] -Package xcolor Warning: Incompatible color definition on input line 456. +Overfull \hbox (180.37665pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [7] Legionella cincinnatiensis Legionella droz +anskii LLAP-1 Legionella erythra[] + [] + +Overfull \hbox (186.12534pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [10] Legionella feeleii Legionella gees +tiana Legionella gratiana[] + [] -Overfull \hbox (140.13583pt too wide) in paragraph at lines 459--459 + +Overfull \hbox (226.36615pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [13] Legionella hackeliae Legionella isra +elensis Legionella jamestowniensis[] + [] + + +Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [16] Legionella jordanis Legionella lans +ingensis Legionella londiniensis[] + [] + + +Overfull \hbox (186.12534pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [19] Legionella maceachernii Legionella mora +vica Legionella nautarum[] + [] + + +Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [22] Legionella oakridgensis Legionella pari +siensis Legionella quateirensis[] + [] + + +Overfull \hbox (209.12009pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [25] Legionella quinlivanii Legionella rubr +ilucens Legionella sainthelensi[] + [] + + +Overfull \hbox (203.3714pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [28] Legionella santicrucis Legionella shak +espearei DSM 23087 Legionella spiritensis[] + [] + + +Overfull \hbox (203.3714pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [31] Legionella steelei Legionella stei +gerwaltii Legionella tucsonensis[] + [] + + +Overfull \hbox (13.6647pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## [34] Legionella waltersii Legionella wors +leiensis[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 288--288 +[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go +rmanii Legionella adelaidensis ... Tatlockia micdadei[] + [] + + +Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [1] Legionella adelaidensis Legionella anisa + Legionella birminghamensis Legionella bozemanae[] + [] + + +Overfull \hbox (255.10959pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [5] Legionella brunensis Legionella cherrii + Legionella cincinnatiensis Legionella erythra[] + [] + + +Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [9] Legionella feeleii Legionella geestiana + Legionella gratiana Legionella hackeliae[] + [] + + +Overfull \hbox (283.85303pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [13] Legionella israelensis Legionella jamestownie +nsis Legionella jordanis Legionella lansingensis[] + [] + + +Overfull \hbox (260.85828pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [17] Legionella londiniensis Legionella maceacherni +i Legionella moravica Legionella nautarum[] + [] + + +Overfull \hbox (278.10434pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [21] Legionella oakridgensis Legionella parisiensis + Legionella quateirensis Legionella quinlivanii[] + [] + + +Overfull \hbox (278.10434pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [25] Legionella rubrilucens Legionella sainthelens +i Legionella santicrucis Legionella spiritensis[] + [] + + +Overfull \hbox (266.60696pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## [29] Legionella steelei Legionella steigerwalt +ii Legionella tucsonensis Legionella waltersii[] + [] + + +Overfull \hbox (197.62271pt too wide) in paragraph at lines 310--310 +[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh +olderia cepacia ... Rickettsiella grylli[] + [] + + +Overfull \hbox (99.89502pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [1] Legionella beliardensis +Legionella clemsonensis[] + [] + + +Overfull \hbox (88.39764pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [3] Legionella drancourtii +Legionella drozanskii[] + [] + + +Overfull \hbox (243.61221pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [5] Legionella dumoffii NY23 +Legionella endosymbiont of Polyplax serrata PsAG[] + [] + + +Overfull \hbox (76.90027pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [7] Legionella fairfieldensis +Legionella fallonii[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [9] Legionella gormanii +Legionella impletisoli[] + [] + + +Overfull \hbox (99.89502pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [11] Legionella longbeachae +Legionella massiliensis[] + [] + + +Overfull \hbox (105.6437pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [13] Legionella micdadei +Legionella nagasakiensis[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [15] Legionella norrlandica +Legionella pneumophila[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [17] Legionella rowbothamii +Legionella saoudiensis[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [19] Legionella shakespearei +Legionella taurinensis[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [21] Legionella tunisiensis +Legionella wadsworthii[] + [] + + +Overfull \hbox (134.38715pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [23] Legionella yabuuchiae +Candidatus Coxiella mudrowiae[] + [] + + +Overfull \hbox (226.36615pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [25] Coxiella burnetii +Coxiella endosymbiont of Amblyomma americanum[] + [] + + +Overfull \hbox (243.61221pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [27] Coxiella endosymbiont of Amblyomma sculptum +Coxiella endosymbiont of Rhipicephalus microplus[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15 +Coxiella sp. DG_40[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [31] Aquicella lusitana +Aquicella siphonis[] + [] + + +Overfull \hbox (168.87927pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [33] Diplorickettsia massiliensis +Candidatus Rickettsiella isopodorum[] + [] + + +Overfull \hbox (82.64896pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [35] Candidatus Rickettsiella viridis +Rickettsiella grylli[] + [] + + +Overfull \hbox (168.87927pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [37] Candidatus Berkiella aquae +Candidatus Berkiella cookevillensis[] + [] + + +Overfull \hbox (82.64896pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## [39] Burkholderia mallei +Burkholderia cepacia[] + [] + + +Overfull \hbox (197.62271pt too wide) in paragraph at lines 337--337 +[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh +olderia cepacia ... Rickettsiella grylli[] + [] + + +Overfull \hbox (65.4029pt too wide) in paragraph at lines 345--345 +[]\OT1/cmtt/m/n/10.95 ## [1] Legionella drozanskii LLAP-1 Legionella shake +spearei DSM 23087[] + [] + + +Overfull \hbox (272.35565pt too wide) in paragraph at lines 345--345 +[]\OT1/cmtt/m/n/10.95 ## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter go +rmanii Legionella adelaidensis ... Tatlockia micdadei[] + [] + +[5] [6] + +Package xcolor Warning: Incompatible color definition on input line 357. + + +Overfull \hbox (140.13583pt too wide) in paragraph at lines 360--360 [][]\OT1/cmtt/m/n/10.95 guptasp[][]<-[][]guptasp[guptasp[] []%in%[] []c[][]([][ ]"Legionella drozanskii"[][],[] []"Legionella shakespearei"[][])[][]==[][]F][][ ] [] -Overfull \hbox (42.40814pt too wide) in paragraph at lines 489--489 +Overfull \hbox (99.89502pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [1] Legionella beliardensis +Legionella clemsonensis[] + [] + + +Overfull \hbox (105.6437pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [3] Legionella drancourtii +Legionella dumoffii NY23[] + [] + + +Overfull \hbox (111.3924pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [5] Legionella endosymbiont of Polyplax serrata PsAG +Legionella fairfieldensis[] + [] + + +Overfull \hbox (76.90027pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [7] Legionella fallonii +Legionella gormanii[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [9] Legionella impletisoli +Legionella longbeachae[] + [] + + +Overfull \hbox (76.90027pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [11] Legionella massiliensis +Legionella micdadei[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [13] Legionella nagasakiensis +Legionella norrlandica[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [15] Legionella pneumophila +Legionella rowbothamii[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [17] Legionella saoudiensis +Legionella taurinensis[] + [] + + +Overfull \hbox (94.14633pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## [19] Legionella tunisiensis +Legionella wadsworthii[] + [] + + +Overfull \hbox (197.62271pt too wide) in paragraph at lines 377--377 +[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh +olderia cepacia ... Rickettsiella grylli[] + [] + + +Overfull \hbox (42.40814pt too wide) in paragraph at lines 380--380 [][]\OT1/cmtt/m/n/10.95 guptasp[][]<-[][]c[][]([][]as.character[][](guptasp[[][ ]grep[][](guptasp,[] []pattern[][]=[][]"Legionella"[][])]),[][] [] -Overfull \hbox (42.40814pt too wide) in paragraph at lines 490--490 +Overfull \hbox (42.40814pt too wide) in paragraph at lines 381--381 [] []\OT1/cmtt/m/n/10.95 as.character[][](guptasp[[][]grep[][](guptasp,[] [] pattern[][]=[][]"Coxiella burnetii"[][])]))[][] [] -Overfull \hbox (277.54225pt too wide) in paragraph at lines 496--496 +Overfull \hbox (277.54225pt too wide) in paragraph at lines 387--387 [][]\OT1/cmtt/m/it/10.95 ## remove \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 te xtit\OMS/cmsy/m/n/10.95 f\OT1/cmtt/m/it/10.95 Fluoribacter dumoffii\OMS/cmsy/m/ n/10.95 g \OT1/cmtt/m/it/10.95 NY 23, \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 @@ -1009,389 +1495,495 @@ n/10.95 g \OT1/cmtt/m/it/10.95 NY 23, \OMS/cmsy/m/n/10.95 n\OT1/cmtt/m/it/10.95 n/10.95 g\OT1/cmtt/m/it/10.95 .[][] [] -[9] -Package xcolor Warning: Incompatible color definition on input line 509. +Package xcolor Warning: Incompatible color definition on input line 400. + +[7] +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## Species Nu +mber_of_Assemblies[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 3 Legionella beliardensis + 2[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 9 Legionella clemsonensis + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 10 Legionella drancourtii + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 13 Legionella endosymbiont of Polyplax serrata PsAG + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 15 Legionella fairfieldensis + 2[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 16 Legionella fallonii + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 22 Legionella impletisoli + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 28 Legionella longbeachae + 9[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 30 Legionella massiliensis + 2[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 33 Legionella nagasakiensis + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 35 Legionella norrlandica + 1[] + [] + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 41 Legionella rowbothamii + 1[] + [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 45 Legionella saoudiensis + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 50 Legionella taurinensis + 16[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 52 Legionella tunisiensis + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 53 Legionella wadsworthii + 3[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 56 Legionella yabuuchiae + 1[] + [] + + +Overfull \hbox (71.15158pt too wide) in paragraph at lines 447--447 +[]\OT1/cmtt/m/n/10.95 ## 58 Coxiella burnetii + 69[] + [] + + +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## Available_Genome_Accession_Number_.Ref_Seq_is_provi ded_when_available.[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 3 NZ_UGNV01000001.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 9 NZ_CP016397.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 10 NZ_JH413847.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 13 NZ_CP021497.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 15 NZ_JHYC01000001.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 16 NZ_LN614827.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 22 N Z_CAAAIA010000001.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 28 NC_013861.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 30 NZ_CCVW01000001.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 33 N Z_CAAAID010000001.1[] [] -Overfull \hbox (76.90027pt too 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(76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 53 NZ_KL370759.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 56 N Z_CAAAIW010000001.1[] [] -Overfull \hbox (76.90027pt too wide) in paragraph at lines 575--575 +Overfull \hbox (76.90027pt too wide) in paragraph at lines 447--447 []\OT1/cmtt/m/n/10.95 ## 58 NZ_CP013667.1[] [] -Overfull \hbox (117.14108pt too wide) in paragraph at lines 577--577 +Overfull \hbox (117.14108pt too wide) in paragraph at lines 449--449 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella beliardensis"[][]][][]<-[][]"GCA_900452395.1"[][] [] -Overfull \hbox (117.14108pt too wide) in paragraph at lines 578--578 +Overfull \hbox (117.14108pt too wide) in paragraph at lines 450--450 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella clemsonensis"[][]][][]<-[][]"GCA_002240035.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 579--579 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 451--451 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella drancourtii"[][]][][]<-[][]"GCA_000162755.2"[][] [] -Overfull \hbox (260.85828pt too wide) in paragraph at lines 580--580 +Overfull \hbox (260.85828pt too wide) in paragraph at lines 452--452 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella endosymbiont of Polyplax serrata PsAG"[][]][][]<-[][]"GCA_00 2776555.1"[][] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 581--581 +Overfull \hbox (128.63846pt too wide) in paragraph at lines 453--453 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella fairfieldensis"[][]][][]<-[][]"GCA_000621525.1"[][] [] -Overfull \hbox (94.14633pt too wide) in paragraph at lines 583--583 +Overfull \hbox (94.14633pt too wide) in paragraph at lines 455--455 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella fallonii"[][]][][]<-[][]"GCA_000953135.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 584--584 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 456--456 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella impletisoli"[][]][][]<-[][]"GCA_900639875.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 585--585 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 457--457 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella longbeachae"[][]][][]<-[][]"GCA_000091785.1"[][] [] -Overfull \hbox (117.14108pt too wide) in paragraph at lines 586--586 +Overfull \hbox (117.14108pt too wide) in paragraph at lines 458--458 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella massiliensis"[][]][][]<-[][]"GCA_000756815.1"[][] [] -Overfull \hbox (122.88977pt too wide) in paragraph at lines 587--587 +Overfull \hbox (122.88977pt too wide) in paragraph at lines 459--459 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella nagasakiensis"[][]][][]<-[][]"GCA_900639915.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 589--589 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 461--461 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella norrlandica"[][]][][]<-[][]"GCA_000770585.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 590--590 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 462--462 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella rowbothamii"[][]][][]<-[][]"GCA_900639985.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 591--591 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 463--463 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella saoudiensis"[][]][][]<-[][]"GCA_001465875.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 592--592 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 464--464 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella taurinensis"[][]][][]<-[][]"GCA_003070665.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 594--594 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 466--466 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella tunisiensis"[][]][][]<-[][]"GCA_000308315.1"[][] [] -Overfull \hbox (111.3924pt too wide) in paragraph at lines 595--595 +Overfull \hbox (111.3924pt too wide) in paragraph at lines 467--467 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella wadsworthii"[][]][][]<-[][]"GCA_000701265.1"[][] [] -Overfull \hbox (105.6437pt too wide) in paragraph at lines 596--596 +Overfull \hbox (105.6437pt too wide) in paragraph at lines 468--468 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Legionella yabuuchiae"[][]][][]<-[][]"GCA_900640115.1"[][] [] -Overfull \hbox (82.64896pt too wide) in paragraph at lines 597--597 +Overfull \hbox (82.64896pt too wide) in paragraph at lines 469--469 [][]\OT1/cmtt/m/n/10.95 guptaonly[][]$[][]Assembly[guptaonly[][]$[][]Species[][ ]==[][]"Coxiella burnetii"[][]][][]<-[][]"GCA_001572745.1"[][] [] -[10] -Underfull \vbox (badness 10000) detected at line 599 - [] - +[8] -Underfull \vbox (badness 10000) detected at line 599 - [] - -[11] +Package xcolor Warning: Incompatible color definition on input line 476. -Package xcolor Warning: Incompatible color definition on input line 604. -[12] -Overfull \hbox (36.65945pt too wide) in paragraph at lines 606--606 +Overfull \hbox (36.65945pt too wide) in paragraph at lines 478--478 [][]\OT1/cmtt/m/n/10.95 tabAsstmp[][]<-[][]cbind[][](guptaonly[][]$[][]Assembly ,[] []as.character[][](guptaonly[][]$[][]Species),[][] [] -Package xcolor Warning: Incompatible color definition on input line 618. +Package xcolor Warning: Incompatible color definition on input line 490. -Overfull \hbox (232.11484pt too wide) in paragraph at lines 620--620 +Overfull \hbox (232.11484pt too wide) in paragraph at lines 492--492 [][]\OT1/cmtt/m/n/10.95 ncbi[][]<-[][]read.table[][]([][]paste0[][](data,[] []" tab_ncbi_file.csv"[][]),[] []sep[][]=[][]";"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char[] []=[] []""[][])[][] [] -Overfull \hbox (295.3504pt too wide) in paragraph at lines 621--621 +Overfull \hbox (295.3504pt too wide) in paragraph at lines 493--493 [][]\OT1/cmtt/m/n/10.95 ncbi2[][]<-[][]read.table[][]([][]paste0[][](data,[] [] "tab_ncbi_contigs_parsed.csv"[][]),[] []sep[][]=[][]";"[][],[] []fill[][]=[][]T RUE[][],[] []header[][]=[][]TRUE[][],[] []comment.char[] []=[] []""[][])[][] [] -LaTeX Font Info: Try loading font information for TS1+cmr on input line 630. +[9] +LaTeX Font Info: Try loading font information for TS1+cmr on input line 502. (/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 630--631 +Overfull \hbox (51.54103pt too wide) in paragraph at lines 502--503 []\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 634--635 +Overfull \hbox (49.38147pt too wide) in paragraph at lines 506--507 []\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 642--643 +Overfull \hbox (52.07639pt too wide) in paragraph at lines 514--515 []\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 645--646 +Overfull \hbox (49.9168pt too wide) in paragraph at lines 517--518 []\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 649--650 +Overfull \hbox (29.24263pt too wide) in paragraph at lines 521--522 []\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 655. +Package xcolor Warning: Incompatible color definition on input line 527. -Overfull \hbox (226.36615pt too wide) in paragraph at lines 673--673 +Overfull \hbox (226.36615pt too wide) in paragraph at lines 545--545 [][]\OT1/cmtt/m/n/10.95 write.table[][](tabAss,[] []paste0[][](home,[] []"/phyl olegio/doc/tabAss.txt"[][]),[] []quote[][]=[][]FALSE[][],[] []row.names[][]=[][ ]FALSE[][],[] []sep[][]=[][]";"[][])[][] [] -[13] +[10] -Package xcolor Warning: Incompatible color definition on input line 696. +Package xcolor Warning: Incompatible color definition on input line 568. -Overfull \hbox (94.14633pt too wide) in paragraph at lines 702--702 +Overfull \hbox (94.14633pt too wide) in paragraph at lines 574--574 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss,[] []c[][]([][]"GCA _001467875.1"[][],[] []"Legionella micdadei"[][],[] []"Pillon"[][]))[][] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 703--703 +Overfull \hbox (128.63846pt too wide) in paragraph at lines 575--575 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_900639865.1"[][],[] []"Legionella gresilensis"[][],[] []"Pillon"[][]))[][] [] -Overfull \hbox (122.88977pt too wide) in paragraph at lines 704--704 +Overfull \hbox (122.88977pt too wide) in paragraph at lines 576--576 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_900461525.1"[][],[] []"Legionella busanensis"[][],[] []"Pillon"[][]))[][] [] -Overfull \hbox (105.6437pt too wide) in paragraph at lines 705--705 +Overfull \hbox (105.6437pt too wide) in paragraph at lines 577--577 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_000236145.1"[][],[] []"Legionella dumoffi"[][],[] []"Pillon"[][]))[][] [] -Overfull \hbox (151.63321pt too wide) in paragraph at lines 706--706 +Overfull \hbox (151.63321pt too wide) in paragraph at lines 578--578 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_003990055.1"[][],[] []"Legionella septentrionalis"[][],[] []"Pillon"[][]))[ ][] [] -Overfull \hbox (128.63846pt too wide) in paragraph at lines 707--707 +Overfull \hbox (128.63846pt too wide) in paragraph at lines 579--579 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_900452385.1"[][],[] []"Legionella donaldsonii"[][],[] []"Pillon"[][]))[][] [] -Overfull \hbox (157.3819pt too wide) in paragraph at lines 708--708 +Overfull \hbox (157.3819pt too wide) in paragraph at lines 580--580 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_001886835.1"[][],[] []"Legionella fraseri Dallas1E"[][],[] []"Pillon"[][])) [][] [] -Overfull \hbox (163.13058pt too wide) in paragraph at lines 709--709 +Overfull \hbox (163.13058pt too wide) in paragraph at lines 581--581 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_003003865.1"[][],[] []"Legionella fraseri Lansing 3"[][],[] []"Pillon"[][]) )[][] [] -Overfull \hbox (186.12534pt too wide) in paragraph at lines 710--710 +Overfull \hbox (186.12534pt too wide) in paragraph at lines 582--582 [][]\OT1/cmtt/m/n/10.95 tabAss_V2[][]<-[][]rbind[][](tabAss_V2,[] []c[][]([][]" GCA_003003755.1"[][],[] []"Legionella fraseri Los Angeles 1"[][],[] []"Pillon"[ ][]))[][] [] -Overfull \hbox (260.85828pt too wide) in paragraph at lines 714--714 +Overfull \hbox (260.85828pt too wide) in paragraph at lines 586--586 [][]\OT1/cmtt/m/n/10.95 write.table[][](tabAss_V2,[] []paste0[][](home,[] []"/p 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PDF statistics: - 258 PDF objects out of 1000 (max. 8388607) - 210 compressed objects within 3 object streams - 41 named destinations out of 1000 (max. 500000) + 229 PDF objects out of 1000 (max. 8388607) + 188 compressed objects within 2 object streams + 35 named destinations out of 1000 (max. 500000) 112 words of extra memory for PDF output out of 10000 (max. 10000000) diff --git a/doc/1_reference_legio_phylo.pdf b/doc/1_reference_legio_phylo.pdf index b537326dc4235616d80a5e27bbd0955b2e4ce10c..e7ccefddc522613c2affb660c2fcefff61386c6e 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 f06946c0d3db0b08792c4bae4213a2650f52a317..047c198051da11d6d5f76877d188d53834dd3f65 100644 --- a/doc/1_reference_legio_phylo.tex +++ b/doc/1_reference_legio_phylo.tex @@ -122,22 +122,14 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti \hlstd{datalist1} \end{alltt} \begin{verbatim} -## [1] "NIHMS817051-supplement-Supplemental_Table_1.csv" -## [2] "NIHMS817051-supplement-Supplemental_Table_1.xlsx" -## [3] "NIHMS817051-supplement-Supplemental_Table_10.csv" -## [4] "NIHMS817051-supplement-Supplemental_Table_10.xlsx" -## [5] "NIHMS817051-supplement-Supplemental_Table_11.xlsx" -## [6] "NIHMS817051-supplement-Supplemental_Table_12.xlsx" -## [7] "NIHMS817051-supplement-Supplemental_Table_2.xlsx" -## [8] "NIHMS817051-supplement-Supplemental_Table_3_tmp.xlsx" -## [9] "NIHMS817051-supplement-Supplemental_Table_3.csv" -## [10] "NIHMS817051-supplement-Supplemental_Table_3.xlsx" -## [11] "NIHMS817051-supplement-Supplemental_Table_4.xlsx" -## [12] "NIHMS817051-supplement-Supplemental_Table_5.xlsx" -## [13] "NIHMS817051-supplement-Supplemental_Table_6.xlsx" -## [14] "NIHMS817051-supplement-Supplemental_Table_7.xlsx" -## [15] "NIHMS817051-supplement-Supplemental_Table_8.xlsx" -## [16] "NIHMS817051-supplement-Supplemental_Table_9.xlsx" +## [1] "NIHMS817051-supplement-Supplemental_Table_1.csv" "NIHMS817051-supplement-Supplemental_Table_1.xlsx" +## [3] "NIHMS817051-supplement-Supplemental_Table_10.csv" "NIHMS817051-supplement-Supplemental_Table_10.xlsx" +## [5] "NIHMS817051-supplement-Supplemental_Table_11.xlsx" "NIHMS817051-supplement-Supplemental_Table_12.xlsx" +## [7] "NIHMS817051-supplement-Supplemental_Table_2.xlsx" "NIHMS817051-supplement-Supplemental_Table_3_tmp.xlsx" +## [9] "NIHMS817051-supplement-Supplemental_Table_3.csv" "NIHMS817051-supplement-Supplemental_Table_3.xlsx" +## [11] "NIHMS817051-supplement-Supplemental_Table_4.xlsx" "NIHMS817051-supplement-Supplemental_Table_5.xlsx" +## [13] "NIHMS817051-supplement-Supplemental_Table_6.xlsx" "NIHMS817051-supplement-Supplemental_Table_7.xlsx" +## [15] "NIHMS817051-supplement-Supplemental_Table_8.xlsx" "NIHMS817051-supplement-Supplemental_Table_9.xlsx" \end{verbatim} \end{kframe} \end{knitrout} @@ -149,20 +141,13 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti \hlkwd{head}\hlstd{(tab1)} \end{alltt} \begin{verbatim} -## Species ATCC.number Strain.designation -## 1 L. adelaidensis ATCC49625 ATCC49625 -## 2 L. anisa ATCC35292 WA-316-C3 -## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 -## 4 L. bozemanii ATCC33217 WIGA -## 5 L. brunensis ATCC43878 ATCC43878 -## 6 L. cherrii ATCC35252 ORW -## Isolation ORF.prefix -## 1 Water in cooling tower (Adelaide, Australia) Lade -## 2 Tap water (Los Angeles, CA, USA) Lani -## 3 Lung biopsy (Alabama, USA) Lbir -## 4 Lung tissue (Key West, FL, USA) Lboz -## 5 Cooling tower water (Czechoslovakia) Lbru -## 6 Thermally altered water (Minnesota, USA) Lche +## Species ATCC.number Strain.designation Isolation ORF.prefix +## 1 L. adelaidensis ATCC49625 ATCC49625 Water in cooling tower (Adelaide, Australia) Lade +## 2 L. anisa ATCC35292 WA-316-C3 Tap water (Los Angeles, CA, USA) Lani +## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 Lung biopsy (Alabama, USA) Lbir +## 4 L. bozemanii ATCC33217 WIGA Lung tissue (Key West, FL, USA) Lboz +## 5 L. brunensis ATCC43878 ATCC43878 Cooling tower water (Czechoslovakia) Lbru +## 6 L. cherrii ATCC35252 ORW Thermally altered water (Minnesota, USA) Lche ## Accession Version BioSample BioProject ## 1 LNKA00000000 LNKA01000000 SAMN03842654 PRJNA285910 ## 2 LNXS00000000 LNXS01000000 SAMN04274764 PRJNA285910 @@ -199,45 +184,20 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti \hlstd{tabAss}\hlopt{$}\hlstd{Taxonomy} \end{alltt} \begin{verbatim} -## [1] Fluoribacter dumoffii NY 23 -## [2] Fluoribacter gormanii -## [3] Legionella adelaidensis -## [4] Legionella anisa -## [5] Legionella birminghamensis -## [6] Legionella bozemanae -## [7] Legionella brunensis -## [8] Legionella cherrii -## [9] Legionella cincinnatiensis -## [10] Legionella drozanskii LLAP-1 -## [11] Legionella erythra -## [12] Legionella feeleii -## [13] Legionella geestiana -## [14] Legionella gratiana -## [15] Legionella hackeliae -## [16] Legionella israelensis -## [17] Legionella jamestowniensis -## [18] Legionella jordanis -## [19] Legionella lansingensis -## [20] Legionella londiniensis -## [21] Legionella maceachernii -## [22] Legionella moravica -## [23] Legionella nautarum -## [24] Legionella oakridgensis -## [25] Legionella parisiensis -## [26] Legionella quateirensis -## [27] Legionella quinlivanii -## [28] Legionella rubrilucens -## [29] Legionella sainthelensi -## [30] Legionella santicrucis -## [31] Legionella shakespearei DSM 23087 -## [32] Legionella spiritensis -## [33] Legionella steelei -## [34] Legionella steigerwaltii -## [35] Legionella tucsonensis -## [36] Legionella waltersii -## [37] Legionella worsleiensis -## [38] Tatlockia micdadei -## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei +## [1] Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis +## [4] Legionella anisa Legionella birminghamensis Legionella bozemanae +## [7] Legionella brunensis Legionella cherrii Legionella cincinnatiensis +## [10] Legionella drozanskii LLAP-1 Legionella erythra Legionella feeleii +## [13] Legionella geestiana Legionella gratiana Legionella hackeliae +## [16] Legionella israelensis Legionella jamestowniensis Legionella jordanis +## [19] Legionella lansingensis Legionella londiniensis Legionella maceachernii +## [22] Legionella moravica Legionella nautarum Legionella oakridgensis +## [25] Legionella parisiensis Legionella quateirensis Legionella quinlivanii +## [28] Legionella rubrilucens Legionella sainthelensi Legionella santicrucis +## [31] Legionella shakespearei DSM 23087 Legionella spiritensis Legionella steelei +## [34] Legionella steigerwaltii Legionella tucsonensis Legionella waltersii +## [37] Legionella worsleiensis Tatlockia micdadei +## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei \end{verbatim} \end{kframe} \end{knitrout} @@ -271,20 +231,13 @@ We keep only legionella, not \textit{Fluoribacter dumoffii} NY 23, \textit{Fluor \hlkwd{head}\hlstd{(gupta1)} \end{alltt} \begin{verbatim} -## Species -## 1 Legionella adelaidensis -## 2 Legionella anisa -## 3 Legionella beliardensis -## 4 Legionella birminghamensis -## 5 Legionella bozemanae -## 6 Legionella brunensis -## Type.Strain -## 1 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735 -## 2 ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3 -## 3 ATCC 700512; CIP 106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1 -## 4 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437 -## 5 ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA -## 6 441-1; ATCC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240 +## Species Type.Strain +## 1 Legionella adelaidensis 1762-Aus-E; ATCC 49625; CCUG 31231 A; CIP 103645; DSM 19888; NCTC 12735 +## 2 Legionella anisa ATCC 35292; CCUG 29665; CIP 103870; DSM 17627; JCM 7573; NCTC 11974; WA-316-C3 +## 3 Legionella beliardensis ATCC 700512; CIP 106632; DSM 19152; Montb\xe9liard A1; Montb\xe9liard A1 +## 4 Legionella birminghamensis 1407-AL-H; ATCC 43702; CCUG 31233 A; CIP 103871; DSM 19232; JCM 7559; NCTC 12437 +## 5 Legionella bozemanae ALLO1; ATCC 33217; CIP 103872; DSM 16523; WIGA +## 6 Legionella brunensis 441-1; ATCC 43878; CCUG 31114; CIP 103874; DSM 19236; NCTC 12240 ## Type.Strain.chosen Type_Strain_Availability Number_of_Assemblies ## 1 1762-Aus-E Y 3 ## 2 <NA> N 5 @@ -319,42 +272,19 @@ Which species are present in gupta not in the previous datasets. \hlstd{species} \end{alltt} \begin{verbatim} -## [1] Legionella adelaidensis -## [2] Legionella anisa -## [3] Legionella birminghamensis -## [4] Legionella bozemanae -## [5] Legionella brunensis -## [6] Legionella cherrii -## [7] Legionella cincinnatiensis -## [8] Legionella drozanskii LLAP-1 -## [9] Legionella erythra -## [10] Legionella feeleii -## [11] Legionella geestiana -## [12] Legionella gratiana -## [13] Legionella hackeliae -## [14] Legionella israelensis -## [15] Legionella jamestowniensis -## [16] Legionella jordanis -## [17] Legionella lansingensis -## [18] Legionella londiniensis -## [19] Legionella maceachernii -## [20] Legionella moravica -## [21] Legionella nautarum -## [22] Legionella oakridgensis -## [23] Legionella parisiensis -## [24] Legionella quateirensis -## [25] Legionella quinlivanii -## [26] Legionella rubrilucens -## [27] Legionella sainthelensi -## [28] Legionella santicrucis -## [29] Legionella shakespearei DSM 23087 -## [30] Legionella spiritensis -## [31] Legionella steelei -## [32] Legionella steigerwaltii -## [33] Legionella tucsonensis -## [34] Legionella waltersii -## [35] Legionella worsleiensis -## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei +## [1] Legionella adelaidensis Legionella anisa Legionella birminghamensis +## [4] Legionella bozemanae Legionella brunensis Legionella cherrii +## [7] Legionella cincinnatiensis Legionella drozanskii LLAP-1 Legionella erythra +## [10] Legionella feeleii Legionella geestiana Legionella gratiana +## [13] Legionella hackeliae Legionella israelensis Legionella jamestowniensis +## [16] Legionella jordanis Legionella lansingensis Legionella londiniensis +## [19] Legionella maceachernii Legionella moravica Legionella nautarum +## [22] Legionella oakridgensis Legionella parisiensis Legionella quateirensis +## [25] Legionella quinlivanii Legionella rubrilucens Legionella sainthelensi +## [28] Legionella santicrucis Legionella shakespearei DSM 23087 Legionella spiritensis +## [31] Legionella steelei Legionella steigerwaltii Legionella tucsonensis +## [34] Legionella waltersii Legionella worsleiensis +## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei \end{verbatim} \begin{alltt} \hlkwd{length}\hlstd{(species)} @@ -367,80 +297,51 @@ Which species are present in gupta not in the previous datasets. \hlstd{gupta1}\hlopt{$}\hlstd{Species[gupta1}\hlopt{$}\hlstd{Species} \hlopt{%in%} \hlstd{species]} \end{alltt} \begin{verbatim} -## [1] Legionella adelaidensis Legionella anisa -## [3] Legionella birminghamensis Legionella bozemanae -## [5] Legionella brunensis Legionella cherrii -## [7] Legionella cincinnatiensis Legionella erythra -## [9] Legionella feeleii Legionella geestiana -## [11] Legionella gratiana Legionella hackeliae -## [13] Legionella israelensis Legionella jamestowniensis -## [15] Legionella jordanis Legionella lansingensis -## [17] Legionella londiniensis Legionella maceachernii -## [19] Legionella moravica Legionella nautarum -## [21] Legionella oakridgensis Legionella parisiensis -## [23] Legionella quateirensis Legionella quinlivanii -## [25] Legionella rubrilucens Legionella sainthelensi -## [27] Legionella santicrucis Legionella spiritensis -## [29] Legionella steelei Legionella steigerwaltii -## [31] Legionella tucsonensis Legionella waltersii +## [1] Legionella adelaidensis Legionella anisa Legionella birminghamensis Legionella bozemanae +## [5] Legionella brunensis Legionella cherrii Legionella cincinnatiensis Legionella erythra +## [9] Legionella feeleii Legionella geestiana Legionella gratiana Legionella hackeliae +## [13] Legionella israelensis Legionella jamestowniensis Legionella jordanis Legionella lansingensis +## [17] Legionella londiniensis Legionella maceachernii Legionella moravica Legionella nautarum +## [21] Legionella oakridgensis Legionella parisiensis Legionella quateirensis Legionella quinlivanii +## [25] Legionella rubrilucens Legionella sainthelensi Legionella santicrucis Legionella spiritensis +## [29] Legionella steelei Legionella steigerwaltii Legionella tucsonensis Legionella waltersii ## [33] Legionella worsleiensis -## 73 Levels: Aquicella lusitana ... Rickettsiella grylli +## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli \end{verbatim} \begin{alltt} \hlcom{# Only in Gupta} \hlstd{gupta1}\hlopt{$}\hlstd{Species[(gupta1}\hlopt{$}\hlstd{Species} \hlopt{%in%} \hlstd{species)}\hlopt{==}\hlnum{FALSE}\hlstd{]} \end{alltt} \begin{verbatim} -## [1] Legionella beliardensis -## [2] Legionella clemsonensis -## [3] Legionella drancourtii -## [4] Legionella drozanskii -## [5] Legionella dumoffii NY23 -## [6] Legionella endosymbiont of Polyplax serrata PsAG -## [7] Legionella fairfieldensis -## [8] Legionella fallonii -## [9] Legionella gormanii -## [10] Legionella impletisoli -## [11] Legionella longbeachae -## [12] Legionella massiliensis -## [13] Legionella micdadei -## [14] Legionella nagasakiensis -## [15] Legionella norrlandica -## [16] Legionella pneumophila -## [17] Legionella rowbothamii -## [18] Legionella saoudiensis -## [19] Legionella shakespearei -## [20] Legionella taurinensis -## [21] Legionella tunisiensis -## [22] Legionella wadsworthii -## [23] Legionella yabuuchiae -## [24] Candidatus Coxiella mudrowiae -## [25] Coxiella burnetii -## [26] Coxiella endosymbiont of Amblyomma americanum -## [27] Coxiella endosymbiont of Amblyomma sculptum -## [28] Coxiella endosymbiont of Rhipicephalus microplus -## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15 -## [30] Coxiella sp. DG_40 -## [31] Aquicella lusitana -## [32] Aquicella siphonis -## [33] Diplorickettsia massiliensis -## [34] Candidatus Rickettsiella isopodorum -## [35] Candidatus Rickettsiella viridis -## [36] Rickettsiella grylli -## [37] Candidatus Berkiella aquae -## [38] Candidatus Berkiella cookevillensis -## [39] Burkholderia mallei -## [40] Burkholderia cepacia -## 73 Levels: Aquicella lusitana ... Rickettsiella grylli +## [1] Legionella beliardensis Legionella clemsonensis +## [3] Legionella drancourtii Legionella drozanskii +## [5] Legionella dumoffii NY23 Legionella endosymbiont of Polyplax serrata PsAG +## [7] Legionella fairfieldensis Legionella fallonii +## [9] Legionella gormanii Legionella impletisoli +## [11] Legionella longbeachae Legionella massiliensis +## [13] Legionella micdadei Legionella nagasakiensis +## [15] Legionella norrlandica Legionella pneumophila +## [17] Legionella rowbothamii Legionella saoudiensis +## [19] Legionella shakespearei Legionella taurinensis +## [21] Legionella tunisiensis Legionella wadsworthii +## [23] Legionella yabuuchiae Candidatus Coxiella mudrowiae +## [25] Coxiella burnetii Coxiella endosymbiont of Amblyomma americanum +## [27] Coxiella endosymbiont of Amblyomma sculptum Coxiella endosymbiont of Rhipicephalus microplus +## [29] Coxiella sp. RIFCSPHIGHO2_12_FULL_42_15 Coxiella sp. DG_40 +## [31] Aquicella lusitana Aquicella siphonis +## [33] Diplorickettsia massiliensis Candidatus Rickettsiella isopodorum +## [35] Candidatus Rickettsiella viridis Rickettsiella grylli +## [37] Candidatus Berkiella aquae Candidatus Berkiella cookevillensis +## [39] Burkholderia mallei Burkholderia cepacia +## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli \end{verbatim} \begin{alltt} \hlcom{# only in Burstein} \hlstd{species[(species} \hlopt{%in%} \hlstd{gupta1}\hlopt{$}\hlstd{Species)}\hlopt{==}\hlnum{FALSE}\hlstd{]} \end{alltt} \begin{verbatim} -## [1] Legionella drozanskii LLAP-1 -## [2] Legionella shakespearei DSM 23087 -## 38 Levels: Fluoribacter dumoffii NY 23 ... Tatlockia micdadei +## [1] Legionella drozanskii LLAP-1 Legionella shakespearei DSM 23087 +## 38 Levels: Fluoribacter dumoffii NY 23 Fluoribacter gormanii Legionella adelaidensis ... Tatlockia micdadei \end{verbatim} \end{kframe} \end{knitrout} @@ -461,28 +362,18 @@ Final list: Remove Legionella drozanskii and Legionella shakespearei and Aquicel \hlstd{guptasp[}\hlkwd{grep}\hlstd{(guptasp,} \hlkwc{pattern}\hlstd{=}\hlstr{"Legionella"}\hlstd{)]} \end{alltt} \begin{verbatim} -## [1] Legionella beliardensis -## [2] Legionella clemsonensis -## [3] Legionella drancourtii -## [4] Legionella dumoffii NY23 -## [5] Legionella endosymbiont of Polyplax serrata PsAG -## [6] Legionella fairfieldensis -## [7] Legionella fallonii -## [8] Legionella gormanii -## [9] Legionella impletisoli -## [10] Legionella longbeachae -## [11] Legionella massiliensis -## [12] Legionella micdadei -## [13] Legionella nagasakiensis -## [14] Legionella norrlandica -## [15] Legionella pneumophila -## [16] Legionella rowbothamii -## [17] Legionella saoudiensis -## [18] Legionella taurinensis -## [19] Legionella tunisiensis -## [20] Legionella wadsworthii +## [1] Legionella beliardensis Legionella clemsonensis +## [3] Legionella drancourtii Legionella dumoffii NY23 +## [5] Legionella endosymbiont of Polyplax serrata PsAG Legionella fairfieldensis +## [7] Legionella fallonii Legionella gormanii +## [9] Legionella impletisoli Legionella longbeachae +## [11] Legionella massiliensis Legionella micdadei +## [13] Legionella nagasakiensis Legionella norrlandica +## [15] Legionella pneumophila Legionella rowbothamii +## [17] Legionella saoudiensis Legionella taurinensis +## [19] Legionella tunisiensis Legionella wadsworthii ## [21] Legionella yabuuchiae -## 73 Levels: Aquicella lusitana ... Rickettsiella grylli +## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli \end{verbatim} \begin{alltt} \hlcom{## Keep only legio and coxiella} @@ -515,44 +406,25 @@ Manual research of reference genomes using gupta1 \hlstd{guptaonly[,}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{5}\hlstd{,}\hlnum{6}\hlstd{)]} \end{alltt} \begin{verbatim} -## Species -## 3 Legionella beliardensis -## 9 Legionella clemsonensis -## 10 Legionella drancourtii -## 13 Legionella endosymbiont of Polyplax serrata PsAG -## 15 Legionella fairfieldensis -## 16 Legionella fallonii -## 22 Legionella impletisoli -## 28 Legionella longbeachae -## 30 Legionella massiliensis -## 33 Legionella nagasakiensis -## 35 Legionella norrlandica -## 41 Legionella rowbothamii -## 45 Legionella saoudiensis -## 50 Legionella taurinensis -## 52 Legionella tunisiensis -## 53 Legionella wadsworthii -## 56 Legionella yabuuchiae -## 58 Coxiella burnetii -## Number_of_Assemblies -## 3 2 -## 9 1 -## 10 1 -## 13 1 -## 15 2 -## 16 1 -## 22 1 -## 28 9 -## 30 2 -## 33 1 -## 35 1 -## 41 1 -## 45 1 -## 50 16 -## 52 1 -## 53 3 -## 56 1 -## 58 69 +## Species Number_of_Assemblies +## 3 Legionella beliardensis 2 +## 9 Legionella clemsonensis 1 +## 10 Legionella drancourtii 1 +## 13 Legionella endosymbiont of Polyplax serrata PsAG 1 +## 15 Legionella fairfieldensis 2 +## 16 Legionella fallonii 1 +## 22 Legionella impletisoli 1 +## 28 Legionella longbeachae 9 +## 30 Legionella massiliensis 2 +## 33 Legionella nagasakiensis 1 +## 35 Legionella norrlandica 1 +## 41 Legionella rowbothamii 1 +## 45 Legionella saoudiensis 1 +## 50 Legionella taurinensis 16 +## 52 Legionella tunisiensis 1 +## 53 Legionella wadsworthii 3 +## 56 Legionella yabuuchiae 1 +## 58 Coxiella burnetii 69 ## Available_Genome_Accession_Number_.Ref_Seq_is_provided_when_available. ## 3 NZ_UGNV01000001.1 ## 9 NZ_CP016397.1 @@ -688,7 +560,7 @@ From a list given by Margaux Pillon \item Legionella septentrionalis GCF-003990055.1 GCA\_003990055.1 Ok \item Legionella donaldsonii GFC-900452385.1 GCA\_900452385.1 Ok \item L. pneumophila fraseri Dallas1E CP017458.1 GCA\_001886835.1 OK - \item L. pneumophila fraseri Lansing 3 CP021257.1 GCA\_003003865.1 Ok + \item L. pneumophila fraseri Lansing 3 CP021257.1 GCA\_003003865.1 Ok \item L. pneumophila fraseri Los Angeles 1 CP021265.1 GCA\_003003755.1 Ok \end{itemize} @@ -765,38 +637,25 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p \begin{alltt} \hlkwd{library}\hlstd{(ape)} -\hlstd{aln}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp/"}\hlstd{)} +\hlstd{aln}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp_V2/"}\hlstd{)} \hlstd{subrep}\hlkwb{<-}\hlkwd{list.files}\hlstd{(aln)} \hlstd{subrep}\hlkwb{<-}\hlstd{subrep[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=subrep,} \hlkwc{pattern}\hlstd{=}\hlstr{"Q5"}\hlstd{)]} \hlstd{subrep} \end{alltt} \begin{verbatim} -## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823" -## [4] "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772" -## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" -## [10] "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711" -## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654" -## [16] "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314" -## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037" -## [22] "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911" -## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" -## [28] "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712" -## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" -## [34] "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399" -## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306" -## [40] "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786" -## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719" -## [46] "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685" -## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" -## [52] "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400" -## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348" -## [58] "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344" -## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338" -## [64] "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334" -## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" -## [70] "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325" -## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" -## [76] "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287" +## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772" +## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711" +## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314" +## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037" "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911" +## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712" +## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399" +## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786" +## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685" +## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400" +## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344" +## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338" "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334" +## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325" +## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287" \end{verbatim} \begin{alltt} \hlstd{cat}\hlkwb{<-}\hlkwd{vector}\hlstd{()} @@ -811,8 +670,10 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p \hlstd{file}\hlkwb{<-}\hlstd{file[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=file,} \hlkwc{pattern}\hlstd{=}\hlstr{"aln"}\hlstd{)]} \hlkwa{if} \hlstd{(}\hlkwd{length}\hlstd{(file)}\hlopt{>}\hlnum{0}\hlstd{)\{} \hlstd{fasta}\hlkwb{<-}\hlkwd{read.dna}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{,subrepcurrent,} \hlstr{"/"}\hlstd{, file),} \hlkwc{format}\hlstd{=}\hlstr{"fasta"}\hlstd{,} \hlkwc{as.character}\hlstd{=}\hlnum{TRUE}\hlstd{)} - \hlkwd{rownames}\hlstd{(fasta)}\hlkwb{<-}\hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{])} - \hlstd{cat}\hlkwb{<-}\hlkwd{c}\hlstd{(cat,} \hlkwd{rownames}\hlstd{(fasta))} + \hlstd{tmprownames}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{grepl}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwc{pattern} \hlstd{=} \hlstr{"pneumo"}\hlstd{),} + \hlkwd{substr}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta)[}\hlkwd{grep}\hlstd{(}\hlkwc{pattern} \hlstd{=} \hlstr{"pneumophila"}\hlstd{,}\hlkwd{rownames}\hlstd{(fasta))],} \hlnum{1}\hlstd{,}\hlnum{31}\hlstd{),} + \hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{]))} + \hlstd{cat}\hlkwb{<-}\hlkwd{c}\hlstd{(cat, tmprownames)} \hlstd{\}} \hlstd{\}} \end{alltt} @@ -907,97 +768,21 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p \hlcom{# make a cat list containing all species names} \hlkwa{for} \hlstd{(subrepcurrent} \hlkwa{in} \hlstd{subrep)\{} -\hlkwd{print}\hlstd{(subrepcurrent)} +\hlcom{#print(subrepcurrent)} \hlstd{file}\hlkwb{<-}\hlkwd{list.files}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{, subrepcurrent))} \hlstd{file}\hlkwb{<-}\hlstd{file[}\hlkwd{grep}\hlstd{(}\hlkwc{x}\hlstd{=file,} \hlkwc{pattern}\hlstd{=}\hlstr{"aln"}\hlstd{)]} \hlkwa{if} \hlstd{(}\hlkwd{length}\hlstd{(file)}\hlopt{>}\hlnum{0}\hlstd{)\{} \hlstd{fasta}\hlkwb{<-}\hlkwd{read.dna}\hlstd{(}\hlkwd{paste0}\hlstd{(aln,} \hlstr{"/"}\hlstd{,subrepcurrent,} \hlstr{"/"}\hlstd{, file),} \hlkwc{format}\hlstd{=}\hlstr{"fasta"}\hlstd{,} \hlkwc{as.character}\hlstd{=}\hlnum{TRUE}\hlstd{)} - \hlkwd{rownames}\hlstd{(fasta)}\hlkwb{<-}\hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{])} - \hlstd{tmp}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{rownames}\hlstd{(tab)} \hlopt{%in%} \hlkwd{rownames}\hlstd{(fasta),} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)} + \hlstd{tmprownames}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{grepl}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwc{pattern} \hlstd{=} \hlstr{"pneumo"}\hlstd{),} + \hlkwd{substr}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta)[}\hlkwd{grep}\hlstd{(}\hlkwc{pattern} \hlstd{=} \hlstr{"pneumophila"}\hlstd{,}\hlkwd{rownames}\hlstd{(fasta))],} \hlnum{1}\hlstd{,}\hlnum{31}\hlstd{),} + \hlkwd{sapply}\hlstd{(}\hlkwd{rownames}\hlstd{(fasta),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)} \hlkwd{strsplit}\hlstd{(x,} \hlkwc{split}\hlstd{=}\hlstr{"."}\hlstd{,} \hlkwc{fixed}\hlstd{=}\hlnum{TRUE}\hlstd{)[[}\hlnum{1}\hlstd{]][}\hlnum{1}\hlstd{]))} + + \hlstd{tmp}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{rownames}\hlstd{(tab)} \hlopt{%in%} \hlstd{tmprownames,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)} \hlstd{tab[,subrepcurrent]}\hlkwb{<-}\hlstd{tmp} \hlstd{\}} \hlstd{\}} \end{alltt} -\begin{verbatim} -## [1] "Q5ZRF4_lpg2928" -## [1] "Q5ZRP4_lpg2836" -## [1] "Q5ZRQ7_lpg2823" -## [1] "Q5ZRT6_lpg2792" -## [1] "Q5ZRV3_lpg2773" -## [1] "Q5ZRV4_lpg2772" -## [1] "Q5ZRV6_lpg2770" -## [1] "Q5ZRW1_lpg2765" -## [1] "Q5ZRX2_lpg2754" -## [1] "Q5ZRZ3_lpg2727" -## [1] "Q5ZS05_lpg2714" -## [1] "Q5ZS08_lpg2711" -## [1] "Q5ZS49_lpg2670" -## [1] "Q5ZS63_lpg2656" -## [1] "Q5ZS65_lpg2654" -## [1] "Q5ZT28_lpg2337" -## [1] "Q5ZT35_lpg2330" -## [1] "Q5ZT51_lpg2314" -## [1] "Q5ZT61_lpg2304" -## [1] "Q5ZT63_lpg2302" -## [1] "Q5ZTX1_lpg2037" -## [1] "Q5ZTX7_lpg2031" -## [1] "Q5ZU05_lpg2003" -## [1] "Q5ZU96_lpg1911" -## [1] "Q5ZUH7_lpg1821" -## [1] "Q5ZUJ7_lpg1801" -## [1] "Q5ZUM6_lpg1767" -## [1] "Q5ZUS0_lpg1722" -## [1] "Q5ZUS8_lpg1714" -## [1] "Q5ZUT0_lpg1712" -## [1] "Q5ZVH3_lpg1467" -## [1] "Q5ZVJ6_lpg1444" -## [1] "Q5ZVJ7_lpg1443" -## [1] "Q5ZVL5_lpg1425" -## [1] "Q5ZVP0_lpg1400" -## [1] "Q5ZVP1_lpg1399" -## [1] "Q5ZVU2_lpg1348" -## [1] "Q5ZVV6_lpg1334" -## [1] "Q5ZVY2_lpg1306" -## [1] "Q5ZWA4_lpg1181" -## [1] "Q5ZWZ6_lpg0937" -## [1] "Q5ZXE5_lpg0786" -## [1] "Q5ZXJ7_lpg0734" -## [1] "Q5ZXK6_lpg0725" -## [1] "Q5ZXL2_lpg0719" -## [1] "Q5ZXN3_lpg0698" -## [1] "Q5ZXP3_lpg0688" -## [1] "Q5ZXP6_lpg0685" -## [1] "Q5ZXZ2_lpg0588" -## [1] "Q5ZY30_lpg0543" -## [1] "Q5ZY59_lpg0513" -## [1] "Q5ZY67_lpg0505" -## [1] "Q5ZY69_lpg0503" -## [1] "Q5ZYH2_lpg0400" -## [1] "Q5ZYL9_lpg0353" -## [1] "Q5ZYM1_lpg0351" -## [1] "Q5ZYM4_lpg0348" -## [1] "Q5ZYM6_lpg0346" -## [1] "Q5ZYM7_lpg0345" -## [1] "Q5ZYM8_lpg0344" -## [1] "Q5ZYM9_lpg0343" -## [1] "Q5ZYN1_lpg0341" -## [1] "Q5ZYN4_lpg0338" -## [1] "Q5ZYN6_lpg0336" -## [1] "Q5ZYN7_lpg0335" -## [1] "Q5ZYN8_lpg0334" -## [1] "Q5ZYP0_lpg0332" -## [1] "Q5ZYP1_lpg0331" -## [1] "Q5ZYP2_lpg0330" -## [1] "Q5ZYP3_lpg0329" -## [1] "Q5ZYP4_lpg0328" -## [1] "Q5ZYP7_lpg0325" -## [1] "Q5ZYQ0_lpg0322" -## [1] "Q5ZYQ3_lpg0319" -## [1] "Q5ZYQ4_lpg0318" -## [1] "Q5ZYQ5_lpg0317" -## [1] "Q5ZYS4_lpg0287" -\end{verbatim} \end{kframe} \end{knitrout} @@ -1032,7 +817,7 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} -\hlstd{treepath}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp/cat.phylip_phyml_tree"}\hlstd{)} +\hlstd{treepath}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"fasta/78Lp_V2/cat.phylip_phyml_tree"}\hlstd{)} \hlstd{tree}\hlkwb{<-}\hlkwd{read.tree}\hlstd{(treepath)} \hlkwd{plot}\hlstd{(}\hlkwd{root}\hlstd{(tree,} \hlkwc{outgroup} \hlstd{=} \hlstr{"Coxiella_burnetii"}\hlstd{))} diff --git a/doc/1_reference_legio_phylo.toc b/doc/1_reference_legio_phylo.toc index 9ddeec57f032e7952b8dabb2229f5477809e463c..8d6b229d571384426462159c68e9e9f4dd52e108 100644 --- a/doc/1_reference_legio_phylo.toc +++ b/doc/1_reference_legio_phylo.toc @@ -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} diff --git a/doc/figure/barplot1-1.pdf b/doc/figure/barplot1-1.pdf index 34e0f2e43d97be30677201ffdfb42ea4be02624e..a65db9c6d3bf74bd04e51e4485322237791085de 100644 Binary files a/doc/figure/barplot1-1.pdf and b/doc/figure/barplot1-1.pdf differ diff --git a/doc/figure/barplot2-1.pdf b/doc/figure/barplot2-1.pdf index 26ccb10e11a1252c6a5471364392cca8efb7a6fd..116e2325df3f91294dc3d2eb257d9112c3c7cb97 100644 Binary files a/doc/figure/barplot2-1.pdf and b/doc/figure/barplot2-1.pdf differ diff --git a/doc/figure/tree-1.pdf b/doc/figure/tree-1.pdf index c82de6dd7583a9703197358968247c2427bd6d9b..3ac19479d557572bb3576b65a6a00e682505cc4a 100644 Binary files a/doc/figure/tree-1.pdf and b/doc/figure/tree-1.pdf differ diff --git a/doc/tabAss_V2.txt b/doc/tabAss_V2.txt index 2fcfba9a87a37179ebbb2f30874c9a03fc5af2bc..3c75a28d7f30c435226dc2239aef40f7d7b199d3 100644 --- a/doc/tabAss_V2.txt +++ b/doc/tabAss_V2.txt @@ -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