treesak 1.53.3__py3-none-any.whl

TreeSAK/TaxaCountStats.R

@@ -0,0 +1,256 @@
+
+################################################################################
+
+# R script for ranking marker proteins for generating concatenated species trees (127 taxa set)
+# Dombrowski et al., 2020
+# Finalized: February 2020
+
+# modified by Weizhi
+# Rscript /Users/songweizhi/PycharmProjects/Sponge_Hologenome/Scripts/TaxaCountStats.R -t treefile_v2.tre -l List_of_trees_2.txt -g mapping_3.txt -x MarkerList.txt -s TaxaCounts_op.txt -r Genes_to_remove.txt -o a.txt
+
+################################################################################
+
+suppressMessages(library(optparse))
+suppressMessages(library(plyr))
+suppressMessages(library(dbplyr))
+suppressMessages(library(dplyr))
+suppressMessages(library(tidyr))
+suppressMessages(library(ggplot2))
+suppressMessages(library(data.table))
+suppressMessages(library(RColorBrewer))
+suppressMessages(library(gplots))
+suppressMessages(library(ape))
+
+####################################### argument parser ######################################
+
+option_list = list(
+  make_option(c("-t", "--tree"),       type="character", help="combined_contree_file"),
+  make_option(c("-l", "--treelist"),   type="character", help="list_of_trees_txt"),
+  make_option(c("-g", "--mapping"),    type="character", help="mapping_txt"),
+  make_option(c("-x", "--markerlist"), type="character", help="marker_list_txt"),
+  make_option(c("-s", "--cstop"),      type="character", help="combined_count_sister_taxa_output"),
+  make_option(c("-r", "--removegene"), type="character", help="genes_to_remove_txt"),
+  make_option(c("-o", "--output"),     type="character", help="output table")); 
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+combined_contree_file         = opt$tree
+list_of_trees_txt             = opt$treelist
+mapping_txt                   = opt$mapping
+marker_list_txt               = opt$markerlist
+combined_count_sister_taxa_op = opt$cstop
+genes_to_remove_txt           = opt$removegene
+output_table                  = opt$output
+
+################################################################################
+
+#rm(list=ls())
+sessionInfo()
+
+################################################################################
+#0.1 setting working directory (!adjust wdir accordingly!)
+################################################################################
+
+# setting working directory (!adjust wdir accordingly!)
+#wdir <- "/Users/songweizhi/Desktop/Anja_paper/Nina/4_151Marker_analyses/127_taxa"
+#wdir <- "/Users/songweizhi/Desktop/Input_folder_to_R"
+#setwd(wdir)
+
+# Weizhi
+# List_of_trees_2.txt                                     id of marker genes (HOGs) (152, mind order)
+# treefile_v2.tre                                         tree corresponding to each marker gene (HOG)
+# mapping_3.txt                                           taxonomy/cluster/group/color for each genome (Domain is higher than cluster)
+# Genes_to_remove.txt                                     basically a list of marker gene ids
+# MarkerList.txt                                          basically a list of marker gene ids (152, mind order)
+# TaxaCounts_151MarkerGenes_ArcRefv5UAP2_129taxa_v5.txt   concatenated output from count_sister_taxa.py
+
+################################################################################
+#1. read in the treefiles (all concatenated in one large document)
+################################################################################
+#read in concatenated tree and list of trees
+tree_order <- read.table(list_of_trees_txt, sep="\t", header=F, fill=TRUE, quote = "")
+
+trees<-read.tree(combined_contree_file)
+
+
+#make a table from taxa labels and count how many taxa are in each tree
+y <- c()
+for(i in 1:length(trees)){
+  x <- length(trees[[i]]$tip.label)
+  y <- rbind (y,x)
+}
+
+Species_in_tree <- as.data.frame(y)
+rownames(Species_in_tree) <- as.character(tree_order$V1)
+colnames(Species_in_tree) <- "NrSpecies"
+#head(Species_in_tree)
+
+################################################################################
+#2. read in taxa mapping files and stats from tom's script 
+################################################################################
+
+#taxa - taxonomy mapping file
+mapping <- read.table(mapping_txt, sep="\t", header=T, fill=TRUE, quote = "", comment.char = "", check.names = FALSE)
+#head(mapping)
+
+#cleanup and shorten mapping file
+mapping_clean <-unique(mapping[,c("Cluster", "Domain")])
+#head(mapping_clean)
+#dim(mapping_clean)
+
+#list of genes to remove because in these trees archaea were not monphyletic
+genes_to_remove <- read.table(genes_to_remove_txt, sep="\t", header=T, fill=TRUE, quote = "")
+
+#list of total markers used in these analyses
+MarkerList <- read.table(marker_list_txt, sep="\t", header=T, fill=TRUE, quote = "")
+
+#read in statistics file from count_sister_taxa.py
+SisterCounts <- read.table(combined_count_sister_taxa_op, sep="\t", header=T, fill=TRUE, quote = "")
+#colnames(SisterCounts)
+
+################################################################################
+#3. transform data
+################################################################################
+#reduce table on and remove hits with low support (0.1 in this case but can be changed)
+SisterCounts_temp0 <- subset(SisterCounts, Normalized2_sum_of_occurances >= 0.1)
+
+#control, whether something is missing in the mapping file, the first setdiff is the relevant one!
+List_taxa <- as.character(unique(SisterCounts_temp0$Group_of_interest))
+#setdiff(List_taxa, mapping$Cluster)
+
+#add in Group Info (i.e. DPANN, Eury, TACK) for Group of interest (needed to define HGT events)
+SisterCounts_temp1 <-  merge(SisterCounts_temp0, mapping_clean, by.x = "Group_of_interest", by.y = "Cluster", all.x = T)
+colnames(SisterCounts_temp1) <- c( "Group_of_interest", "MarkerID", "Sister_taxa", "Normalized_sum_of_occurances","splits","Normalized2_sum_of_occurances","Clusters", "Group_of_interest_Group")
+#head(SisterCounts_temp1)
+
+#add in Group Info (i.e. DPANN, Eury, TACK) for Sister_taxa (needed to define HGT events)
+SisterCounts_temp2 <-  merge(SisterCounts_temp1, mapping_clean, by.x = "Sister_taxa", by.y = "Cluster", all.x = T)
+colnames(SisterCounts_temp2) <- c( "Sister_taxa", "Group_of_interest", "MarkerID","Normalized_sum_of_occurances", "splits","Normalized2_sum_of_occurances","Clusters","Group_of_interest_Group", "Sister_taxon_Group")
+#head(SisterCounts_temp2)
+
+#resort dataframe for aesthetics
+SisterCounts_temp3 <- SisterCounts_temp2[,c("MarkerID","Group_of_interest", "Group_of_interest_Group", "Sister_taxa", "Sister_taxon_Group", "Normalized_sum_of_occurances","splits", "Normalized2_sum_of_occurances","Clusters")]
+#head(SisterCounts_temp3)
+
+#count nr of total splits
+SisterCounts_temp4 <- cbind(SisterCounts_temp3, count.fields(textConnection(as.character(SisterCounts_temp3$Clusters)), sep = ","))
+#head(SisterCounts_temp4)
+
+#make new column and make a remark whether clusters of interest are split or not
+#Notice: The column "Clusters" lists if there is a split (i.e. if UAP2 12 then all 12 MAGs are together, if UAP2 has 8,4 then UAP2 is split once with one cluster with 8 and the other with 4 taxa)
+SisterCounts_temp4$SplitGroups<- ifelse(grepl(",",SisterCounts_temp3$Clusters), "split", "no")
+#head(SisterCounts_temp4)
+
+#rename a column for better readability
+names(SisterCounts_temp4)[names(SisterCounts_temp4) == "count.fields(textConnection(as.character(SisterCounts_temp3$Clusters)), "] <- 'NrSplits'
+#head(SisterCounts_temp4)
+
+#remove dublicates and keep the Group_of_interest with the best Normalized2_sum_of_occurances value
+#this is done to only have one hits per arcog and group of interest to better normalize the data by the total nr of arcogs and do have a consistent link to the total number of phylogenetic clusters
+SisterCounts_best <-
+  SisterCounts_temp4 %>%
+  group_by(MarkerID,Group_of_interest) %>%
+  filter(Normalized2_sum_of_occurances == max(Normalized2_sum_of_occurances)) 
+
+#count nr of taxonomic groups (i.e. clusters)  in each tree
+Nr_clusters <- Number_of_taxa <- ddply(SisterCounts_best, .(MarkerID), summarize, NrClusters = length(Group_of_interest))
+#head(Nr_clusters)
+
+#merge nr of clusters and nr of species with datatable
+SisterCounts_best_temp1 <- merge(SisterCounts_best, Nr_clusters, by = "MarkerID")
+SisterCounts_best_temp2 <- merge(SisterCounts_best_temp1,Species_in_tree, by.x = "MarkerID", by.y = "row.names" )
+#head(SisterCounts_best_temp2)
+
+#print table          
+# write.table(SisterCounts_best_temp1, "2_Output/Taxa_Summary_1.txt",  sep = "\t", row.names = F, quote =F)
+
+################################################################################
+#4. summarize split events to be able to rank marker genes
+################################################################################
+#summarize splits/cluster
+Split_counts <- ddply(SisterCounts_best_temp1, .(MarkerID,SplitGroups, NrClusters), summarise, quantity = length(NrSplits))
+Split_counts_wide <- spread(Split_counts, SplitGroups, quantity)
+
+#make new column to calulate the percentage of split clusters
+Split_counts_wide$SplitsPerCluster <- round((Split_counts_wide$split/Split_counts_wide$NrClusters)*100, digits = 1)
+#head(Split_counts_wide)
+
+#summarize and coun the total number of splits
+Split_Total <- ddply(SisterCounts_best_temp1, .(MarkerID, NrClusters), summarise, TotalSplits = sum(NrSplits))
+#head(Split_Total)
+
+#combine the two dataframes generated above
+#Summary_temp1 <- merge(Split_counts_wide[,c("MarkerID","NrClusters","SplitsPerCluster")],HGT_Counts, by = "MarkerID" )
+Summary_temp2 <- merge(Split_counts_wide[,c("MarkerID","NrClusters","SplitsPerCluster")], Split_Total, by = "MarkerID")
+Summary_temp3 <- merge(Summary_temp2, Species_in_tree, by.x = "MarkerID", by.y = "row.names")
+Summary_temp3$TotalSplits_to_Species <- round((Summary_temp3$TotalSplits/Summary_temp3$NrSpecies)*100, digits = 1)
+#head(Summary_temp3)
+
+#subset to only print relevant info 
+Summary_temp4 <- Summary_temp3[,c("MarkerID","NrSpecies", "NrClusters.x", "SplitsPerCluster","TotalSplits", "TotalSplits_to_Species" )]
+#head(Summary_temp4)
+
+#if genes were lost already during the tree building step, add that info in
+Summary_temp5 <- merge(MarkerList, Summary_temp4, by = "MarkerID", all.x = T)
+#head(Summary_temp5)
+
+################################################################################
+#5. find highest/lowest 25/50% ranking markers
+################################################################################
+#make vector of genes that are not good marker genes based on literature and that are not monophyletic
+genes_to_remove_vector <- as.character(genes_to_remove$MarkerID) 
+#genes_to_remove_vector
+
+#remove genes from dataframe
+Stats_temp1A <- Summary_temp4[ ! Summary_temp4$MarkerID %in% genes_to_remove_vector, ]
+#dim(Summary_temp4)
+#dim(Stats_temp1A)
+
+#define a cutoff to remove gene trees that have less than 50% of the species as we do not want to use these genes for concatenations
+cutoff <- mean(Stats_temp1A$NrSpecies)/2
+#cutoff
+
+#remove genes that have few species
+Stats_temp1B <- subset(Stats_temp1A, Stats_temp1A[ , "NrSpecies"] > cutoff) 
+#dim(Stats_temp1A)
+#dim(Stats_temp1B)
+
+#rank according to the split clusters in percentage from 1 to xx (lowest/best value = lowest nr) = RankA
+Stats_temp2 <- Stats_temp1B %>% mutate(RankA = rank(SplitsPerCluster, ties.method = 'first'))
+
+#rank according to the total splits normalized by the total number of species from 1 to xx (lowest value = lowest nr)
+Stats_temp3 <- Stats_temp2 %>% mutate(RankB = rank(TotalSplits_to_Species, ties.method = 'first'))
+
+#combine RankA and RankB to get the best for each method
+Stats_temp3$RankA_B <- Stats_temp3$RankA+Stats_temp3$RankB
+#dim(Stats_temp3)
+
+#define the concatenated marker sets and create vectors
+nr_genes <- length(Stats_temp3$MarkerID)
+cutoff_25perc <- round(nr_genes/4, digits = 0)
+cutoff_50perc<- round(nr_genes/2, digits = 0)
+#cutoff_25perc
+#cutoff_50perc
+
+#subset the tables for the different cutoffs
+best_50perc <- as.data.frame(Stats_temp3 %>% top_n(-cutoff_50perc, RankA_B))
+Stats_temp3$best_50perc <- best_50perc$MarkerID[match(Stats_temp3$MarkerID, best_50perc$MarkerID)]
+
+best_25perc <- Stats_temp3 %>% top_n(-cutoff_25perc, RankA_B)
+Stats_temp3$best_25perc <- best_25perc$MarkerID[match(Stats_temp3$MarkerID, best_25perc$MarkerID)]
+
+worst_50perc <- Stats_temp3 %>% top_n(cutoff_50perc, RankA_B)
+Stats_temp3$worst_50perc <-  worst_50perc$MarkerID[match(Stats_temp3$MarkerID, worst_50perc$MarkerID)]
+
+worst_25perc <- Stats_temp3 %>% top_n(cutoff_25perc, RankA_B)
+Stats_temp3$worst_25perc <-   worst_25perc$MarkerID[match(Stats_temp3$MarkerID, worst_25perc$MarkerID)]
+
+Stats_temp3$FullSet <- Stats_temp3$MarkerID
+
+#merge with original table (to keep the statistics)
+Stats_temp4 <- merge(Summary_temp5, Stats_temp3[,c("MarkerID", "RankA", "RankB", "RankA_B", "FullSet", "best_50perc", "best_25perc", "worst_50perc","worst_25perc")], by = "MarkerID", all.x = T)
+
+#print
+write.table(Stats_temp4, output_table, sep = "\t", row.names = F, quote =F, na = "")
+

TreeSAK/TaxonTree.py

@@ -0,0 +1,47 @@
+import argparse
+from ete3 import Tree
+
+
+TaxonTree_usage = '''
+================================ TaxonTree example commands ================================
+
+TreeSAK TaxonTree -i ar53_r220.tree -tax o__Nitrososphaerales -o o__Nitrososphaerales.tree
+
+============================================================================================
+'''
+
+
+def TaxonTree(args):
+
+    tree_file_in     = args['i']
+    interested_taxon = args['tax']
+    tree_file_out    = args['o']
+
+    input_tree = Tree(tree_file_in, quoted_node_names=True, format=1)
+
+    matched_node_list = []
+    for node in input_tree.traverse():
+        if (node.name == interested_taxon) or (interested_taxon in node.name):
+            matched_node_list.append(node.name)
+
+    if len(matched_node_list) == 1:
+        for node in input_tree.traverse():
+            if node.name in matched_node_list:
+                node.write(outfile=tree_file_out)
+    else:
+        print('There are multiple matched nodes. program exited!')
+        print('Matched nodes: %s' % ','.join(matched_node_list))
+        exit()
+
+    print('Subset tree exported to: %s' % tree_file_out)
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    TaxonTree_parser = argparse.ArgumentParser()
+    TaxonTree_parser.add_argument('-i',   required=True,  help='input tree file')
+    TaxonTree_parser.add_argument('-tax', required=True,  help='interested taxon')
+    TaxonTree_parser.add_argument('-o',   required=True,  help='output tree file')
+    args = vars(TaxonTree_parser.parse_args())
+    TaxonTree(args)

TreeSAK/TreeSAK_config.py

@@ -0,0 +1,32 @@
+import os
+
+# extract path to the config file
+pwd_config_file = os.path.realpath(__file__)
+config_file_path = '/'.join(pwd_config_file.split('/')[:-1])
+
+# specify full path to corresponding executables at the right side of colon
+config_dict = {'config_file_path'       : config_file_path,
+               'prodigal'               : 'prodigal',
+               'hmmsearch'              : 'hmmsearch',
+               'hmmfetch'               : 'hmmfetch',
+               'hmmalign'               : 'hmmalign',
+               'hmmstat'                : 'hmmstat',
+               'mafft'                  : 'mafft',
+               'bowtie2'                : 'bowtie2',
+               'bowtie2_build'          : 'bowtie2-build',
+               'blastp'                 : 'blastp',
+               'blastn'                 : 'blastn',
+               'makeblastdb'            : 'makeblastdb',
+               'fasttree'               : 'FastTree',
+               'ranger_mac'             : '%s/Ranger-DTL-Dated.mac'           % config_file_path,
+               'ranger_linux'           : '%s/Ranger-DTL-Dated.linux'         % config_file_path,
+               'path_to_hmm'            : '%s/MetaCHIP_phylo.hmm'             % config_file_path,
+               'circos_HGT_R'           : '%s/MetaCHIP_circos_HGT.R'          % config_file_path,
+               'VisHPD95_R'             : '%s/VisHPD95.R'                     % config_file_path,
+               'label_tree_R'           : '%s/label_tree.R'                   % config_file_path,
+               'cdd2cog_perl'           : '%s/cdd2cog.pl'                     % config_file_path,
+               'get_sankey_plot_R'      : '%s/get_sankey_plot.R'              % config_file_path,
+               'compare_trees_R'        : '%s/compare_trees.R'                % config_file_path,
+               'ko00001_keg'            : '%s/ko00001.keg'                    % config_file_path,
+               'MetaCyc_rxns_with_ec'   : '%s/MetaCyc_reactions_with_ec.txt'  % config_file_path
+               }

TreeSAK/VERSION

@@ -0,0 +1,164 @@
+1.53.3
+- fixed bugs
+
+1.53.0
+- new module added: batch_itol
+
+1.52.0
+- new module added: filter_rename_ar53
+
+1.51.0
+- new module added: iTOL_msa_stats
+
+1.50.0
+- new module added: RootTreeGTDB226
+
+1.49.0
+- new module added: mcmctree_vs_reltime
+
+1.48.0
+- new module added: parse_reltime
+
+1.47.0
+- new module added: GeneTree
+
+1.46.0
+- new module added: cogTree
+
+1.45.0
+- new module added: iTOL_gene_tree
+
+1.44.0
+- new module added: koTree
+
+1.43.0
+- new module added: ALE7
+
+1.42.0
+- new module added: mcmc2tree
+
+1.41.0
+- new module added: mcmcTC
+
+1.40.0
+- new module added: TaxonTree
+
+1.39.0
+- new module added: supertree
+
+1.38.0
+- new module added: pruneMSA
+
+1.37.0
+- new module added: recode
+
+1.36.0
+- new module added: gap_stats
+
+1.35.0
+- new module added: AssessPB
+
+1.34.0
+- new module added: PB
+
+1.33.0
+- new module added: RootTreeGTDB214 and RootTreeGTDB220
+
+1.32.0
+- new module added: replace_clade
+
+1.31.0
+- new module added: PhyloBiAssoc
+
+1.30.0
+- new module added: ALE6
+
+1.29.0
+- new module added: LcaToLeaves
+
+1.28.0
+- new module added: SingleAleHGT
+
+1.27.0
+- new module added: ConcateMSA
+
+1.26.0
+- new module added: pRTC
+
+1.25.0
+- new module added: BMGE
+
+1.24.0
+- new module added: AlignmentPruner
+
+1.23.0
+- new module added: RootTree
+
+1.22.0
+- new module added: OMA2
+
+1.21.0
+- new module added: print_leaves
+
+1.20.0
+- new module added: ALE1, ALE2, ALE3, ALE4
+
+1.19.0
+- new module added: OMA
+
+1.18.0
+- new module added: ExtractMarkerSeq
+
+1.17.0
+- new module added: MarkerSeq2Tree
+
+1.16.0
+- new module added: SplitScoreStep1 and SplitScoreStep2
+
+1.15.0
+- new module added: SingleLinePhy
+
+1.14.0
+- new module added: PMSF
+
+1.13.0
+- new module added: VisHPD95
+
+1.12.0
+- new module added: PlotMcmcNode
+
+1.11.0
+- new module added: CompareMCMC
+
+1.10.0
+- new module added: fa2phy
+
+1.9.0
+- new module added: Dating
+
+1.8.0
+- new module added: AssessMarkerDeltaLL
+
+1.7.0
+- new module added: AssessMarkerPA
+
+1.6.0
+- new module added: Marker2Tree
+
+1.5.0
+- new module added: SliceMSA
+
+1.4.0
+- new module added: ConvertMSA
+
+1.3.0
+- new module added: get_arCOG_seq
+
+1.2.0
+- new module added: parse_deltall_stdout
+
+1.1.0
+- new module added: AssessCVG
+
+1.0.0
+- initial release

TreeSAK/VisHPD95.R

@@ -0,0 +1,45 @@
+library(ggplot2)
+library(optparse)
+
+
+plot_grouped_HPD95 <- function(data_file, plot_width, plot_height, plot_file){
+
+  dat <- read.table(data_file, header = T)
+
+  ggplot(dat, aes(x = Var, y = Mean, ymin = Low, ymax = High)) +
+    geom_pointrange(aes(col = factor(Test), shape=factor(Shape)),
+                    position=position_dodge(width=0.6),                         # controls distance between groups
+                    linewidth = 0.9,                                            # line width
+                    size=0.75) +                                                # size of shape
+    theme_bw() +                                                                # remove background
+    theme(panel.grid.major=element_blank(),                                     # remove grid
+          panel.grid.minor=element_blank()) +                                   # remove grid
+    xlab("") +                                                                  # x-axis label text
+    ylab("95% HPD CI") +                                                        # y-axis label text
+    theme(axis.text.x=element_text(size=12, color='black', angle=30, hjust=1),  # x-axis label, rotate at an angle of 45
+          axis.text.y=element_text(size=12, color='black'),                     # y-axis label
+          legend.text=element_text(size=10)) +                                  # legend label
+    scale_color_discrete(name="Color") +                                        # customize color legend, title
+    guides(color=guide_legend(override.aes=list(linetype=0))) +                 # customize color legend
+    scale_shape_discrete(name="Shape") +                                        # customize color legend, title
+    guides(shape=guide_legend(override.aes=list(linetype=0, color='grey')))     # customize color legend,
+
+  # write to file
+  ggsave(plot_file, width=plot_width, height=plot_height, dpi=300)
+}
+
+
+option_list = list(
+  make_option(c("-i", "--datain"),  type="character", default=NULL, help="input data matrix"),
+  make_option(c("-x", "--width"),   type="double",    default=8,    help="plot width"),
+  make_option(c("-y", "--height"),  type="double",    default=5,    help="plot height"),
+  make_option(c("-o", "--plotout"), type="character", default=NULL, help="output plot"));
+
+opt_parser      = OptionParser(option_list=option_list);
+opt             = parse_args(opt_parser);
+data_matrix_txt = opt$datain
+plot_width      = opt$width
+plot_height     = opt$height
+output_plot     = opt$plotout
+
+plot_grouped_HPD95(data_matrix_txt, plot_width, plot_height, output_plot)