From e112ad439d5685f883d75acff76622f93496f6ae Mon Sep 17 00:00:00 2001 From: Aitor Blanco Date: Tue, 23 Aug 2022 09:34:27 +0200 Subject: [PATCH] Updates to version 4.0.0 --- README.md | 2 +- bioconda_recipe/meta.yaml | 2 +- metaphlan/metaphlan.py | 2 +- metaphlan/strainphlan.py | 2 +- metaphlan/utils/add_metadata_tree.py | 2 +- metaphlan/utils/calculate_diversity.R | 262 ++++++++++++++++++ metaphlan/utils/calculate_unifrac.R | 67 ----- metaphlan/utils/external_exec.py | 2 +- metaphlan/utils/extract_markers.py | 2 +- metaphlan/utils/merge_metaphlan_tables.py | 101 ++++--- ...mpa_v30_CHOCOPhlAn_201901_species_tree.nwk | 1 - ...wk => mpa_vJan21_CHOCOPhlAnSGB_202103.nwk} | 0 ..._vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv} | 0 metaphlan/utils/parallelisation.py | 2 +- metaphlan/utils/plot_tree_graphlan.py | 2 +- metaphlan/utils/sample2markers.py | 2 +- metaphlan/utils/sgb_to_gtdb_profile.py | 6 +- metaphlan/utils/strain_transmission.py | 2 +- metaphlan/utils/util_fun.py | 2 +- setup.py | 2 +- 20 files changed, 328 insertions(+), 135 deletions(-) create mode 100644 metaphlan/utils/calculate_diversity.R delete mode 100644 metaphlan/utils/calculate_unifrac.R delete mode 100644 metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk rename metaphlan/utils/{mpa_v4beta_Jan21_SGB_tree.nwk => mpa_vJan21_CHOCOPhlAnSGB_202103.nwk} (100%) rename metaphlan/utils/{Jan21_SGB2GTDB.tsv => mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv} (100%) diff --git a/README.md b/README.md index 3994e55..4ce7422 100755 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ## Description MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling. -MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them taxonomically unidentified at the species level, allowing: +MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them taxonomically unidentified at the species level (the latest marker information file can be found [here](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt.bz2)), allowing: * unambiguous taxonomic assignments; * an accurate estimation of organismal relative abundance; diff --git a/bioconda_recipe/meta.yaml b/bioconda_recipe/meta.yaml index 89de896..79a8cdd 100644 --- a/bioconda_recipe/meta.yaml +++ b/bioconda_recipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphlan" %} -{% set version = "4.beta" %} +{% set version = "4.0" %} package: name: {{ name }} diff --git a/metaphlan/metaphlan.py b/metaphlan/metaphlan.py index ca4a777..7ff4369 100755 --- a/metaphlan/metaphlan.py +++ b/metaphlan/metaphlan.py @@ -4,7 +4,7 @@ 'Nicola Segata (nicola.segata@unitn.it), ' 'Duy Tin Truong, ' 'Francesco Asnicar (f.asnicar@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import sys diff --git a/metaphlan/strainphlan.py b/metaphlan/strainphlan.py index 4397fb0..e3a7619 100755 --- a/metaphlan/strainphlan.py +++ b/metaphlan/strainphlan.py @@ -4,7 +4,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' diff --git a/metaphlan/utils/add_metadata_tree.py b/metaphlan/utils/add_metadata_tree.py index 8c4a6a2..2b02c18 100755 --- a/metaphlan/utils/add_metadata_tree.py +++ b/metaphlan/utils/add_metadata_tree.py @@ -1,7 +1,7 @@ #!/usr/bin/env python __author__ = ('Duy Tin Truong (duytin.truong@unitn.it), ' 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import argparse as ap diff --git a/metaphlan/utils/calculate_diversity.R b/metaphlan/utils/calculate_diversity.R new file mode 100644 index 0000000..3f48b97 --- /dev/null +++ b/metaphlan/utils/calculate_diversity.R @@ -0,0 +1,262 @@ +#!/usr/bin/env Rscript + +### calculate diversity ### + +# install required packages + +required_pkg <- c("optparse", "ape", "rbiom", "compositions", "BiocManager") +a <- sapply(required_pkg, function(x) { if (!requireNamespace(x, quietly = TRUE)) + install.packages(x, repos = "http://cran.us.r-project.org") +}) +if (! "microbiome" %in% installed.packages()){ + BiocManager::install("microbiome") +} + +# accept arguments from command line + +library("optparse") + +option_list = list( + + make_option(c("-f", "--file"), action="store", type="character", default=NULL, + help="Merged MetaPhlAn profiles. + A table with samples as columns and species as rows is required.", + metavar="character"), + + make_option(c("-o", "--out_directory"), action="store", type="character", default="diversity_analysis", + help="output directory. + [default = %default]"), + + make_option(c("-p", "--outfile_prefix"), action="store", type="character", default=NULL, + help="file name prefix of the output distance matrix and log files. + [default = input file basename]"), + + make_option(c("-t", "--tree"), action="store", type="character", default=NULL, + help="Full path to the MetaPhlAn species Newick tree. + Mandatory for computing UniFrac distances."), + + make_option(c("-d", "--diversity"), action="store", type="character", default="beta", + help="Choose whether to calculate alpha or beta diversity. + Options are alpha or beta. + [default = %default]"), + + make_option(c("-m", "--metric"), action="store", type="character", default="bray-curtis", + help="Name of the function to use when calculating diversity. + Options for alpha diversity are richness, shannon, simpson, gini. + Options for beta diversity are bray-curtis, jaccard, weighted-unifrac, unweighted-unifrac, clr, aitchison. + [default = %default]"), + + make_option(c("-s", "--taxon_separator"), action="store", type="character", default="t__", + help="taxon separator used in the input MetaPhlAn table. + Options are: t__ for MetaPhlAn4 profiles and s__ for MetaPhlAn3 profiles. + [default = %default]") +); + +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); + +if (is.null(opt$file)){ + print_help(opt_parser) + stop('At least one argument must be supplied (input file).tsv', call.=FALSE) +} + +if(! (opt$diversity %in% c('alpha', 'beta'))){ + write(paste0('Method "', opt$diversity, '" not available!'), stdout()) + write(paste0('Available diversity analyses are "alpha" and "beta"'), stdout()) + quit(status = -1) +} + +if(opt$diversity =="alpha" & ! (opt$metric %in% c('richness', 'shannon', 'simpson', 'gini'))){ + write(paste0('Method "', opt$metric, '" not available for alpha diversity'), stdout()) + write(paste0('Available alpha-diversity metrics are "richness", shannon", "simpson", "gini".'), stdout()) + quit(status = -1) +} + +if(opt$diversity =="beta" & ! (opt$metric %in% c('bray-curtis', 'jaccard', 'weighted-unifrac', 'unweighted-unifrac', 'clr', 'aitchison'))){ + write(paste0('Method "', opt$metric, '" not available for beta diversity'), stdout()) + write(paste0('Available beta-diversity distance functions are "bray-curtis", "jaccard", "weighted-unifrac", "unweighted-unifrac", "clr", "aitchison".'), stdout()) + quit(status = -1) +} + +if(! (opt$taxon_separator %in% c('t__', 's__'))){ + write(paste0('Taxon separator "', opt$taxon_separator, '" is not available'), stdout()) + write(paste0('Possible taxon separators are "t__" for MetaPhlAn4 profiles and "s__" for MetaPhlAn3 profiles.'), stdout()) + quit(status = -1) +} + +if(is.null(opt$tree) & grepl('unifrac', opt$metric)){ + write(paste0('Selected beta-diversity metric: "', opt$metric, '"'), stdout()) + stop("A tree is mandatory for computing UniFrac distances. (input tree).nwk", call.=FALSE) +} + +for(x in c(opt$file, opt$tree)){ + if(!file.exists(x)){ + stop(paste0('Input file "', x, '" does not exist!'), call.=FALSE) + } +} + +if(is.null(opt$outfile_prefix)){ + outfile_prefix <- basename(opt$file) + outfile_prefix <- tools::file_path_sans_ext(outfile_prefix) +} else { + outfile_prefix <- opt$outfile_prefix +} + +current_dir <- getwd() +dir.create(file.path(current_dir, opt$out_directory), showWarnings = FALSE) + +outfile <- paste(current_dir, opt$out_directory, outfile_prefix, sep="/") + +### table preprocessing ### + +mpa_table <- read.table(opt$file, comment.char = '#', sep = '\t', header = TRUE, check.names=FALSE) + +# check if NCBI id is present + +vec <- grepl("ncbi", colnames(mpa_table), ignore.case=TRUE) +if(any(vec)){ + # keep all the columns except the one with NCBI id + mpa_table <- mpa_table[grep(opt$taxon_separator, mpa_table[,1]), !vec] +} else { + mpa_table <- mpa_table[grep(opt$taxon_separator, mpa_table[,1]),] +} + +if(opt$taxon_separator == "t__"){ + mpa_table[,1] <- gsub(".+\\|t__SGB", "", mpa_table[,1]) +} else { + mpa_table[,1] <- gsub(".+\\|s__", "", mpa_table[,1]) +} + +mpa_table[,1] <- gsub("_group$", "", mpa_table[,1]) +rownames(mpa_table) <- mpa_table[,1] +mpa_table <- mpa_table[,-1] + +# remove samples with all unknowns +removed <- which(colSums(mpa_table) == 0) + +if(length(removed)>0){ + + if(length(removed)==1){ + message = "# WARNING: 1 sample with 100% unknown species was removed from the input table." + } else { + message = paste0("# WARNING: ", length(removed), " samples with 100% unknown species were removed from the input table.") + } + + write(message, stdout()) + write(paste(names(removed), collapse='\n'), stdout()) + + write(message, file=paste0(outfile, '_samples.log')) + write(paste(names(removed), collapse='\n'), file=paste0(outfile, '_samples.log'), append = TRUE) + + # remove samples + mpa_table <- mpa_table[, -removed] +} + +### Data transformation +mpa_table <- mpa_table / 100 + + +### Beta diversity ### + +if (opt$diversity == "beta"){ + + # Bray-Curtis + if (opt$metric == "bray-curtis"){ + mat <- rbiom::beta.div(as.matrix(mpa_table), method="bray-curtis", weighted=TRUE) + } + + # Jaccard + if (opt$metric == "jaccard"){ + mat <- rbiom::beta.div(as.matrix(mpa_table), method="jaccard", weighted=FALSE) + } + + # Unifrac + if (grepl("unifrac", opt$metric)){ + mpa_tree <- ape::read.tree(opt$tree) + + if(opt$taxon_separator == "s__"){ + mpa_tree$tip.label <- gsub(".+\\|s__", "", mpa_tree$tip.label) + } + + removed <- setdiff(rownames(mpa_table), mpa_tree$tip.label) + + if(length(removed)){ + message = paste0("# WARNING: ", length(removed), " species not present in the tree were removed from the input profile.") + write(message, stdout()) + write(paste(removed, collapse='\n'), stdout()) + + write(message, file=paste0(outfile, '_species.log')) + write(paste(removed, collapse='\n'), file=paste0(outfile, '_species.log'), append = TRUE) + } + filt_tree <- ape::keep.tip(mpa_tree, setdiff(rownames(mpa_table), removed)) + filt_mpa_table <- mpa_table[filt_tree$tip.label,] + + # check again if after species removal some samples have 0s for all the remaining species, and remove them + removed <- which(colSums(filt_mpa_table) == 0) + + if(length(removed)){ + message = paste0("# WARNING: after removal of species not in the tree, ", length(removed), " samples with 0 abundance of the remaining species were removed from the input table.") + + write(message, stdout()) + write(paste(names(removed), collapse='\n'), stdout()) + + if(file.exists(paste0(outfile, '_samples.log'))){ + write(message, file=paste0(outfile, '_samples.log'), append = TRUE) + } else { + write(message, file=paste0(outfile, '_samples.log')) + } + + write(paste(names(removed), collapse='\n'), file=paste0(outfile, '_samples.log'), append = TRUE) + + # remove samples + filt_mpa_table <- filt_mpa_table[, -removed] + } + + if (opt$metric == "weighted-unifrac"){ + mat <- rbiom::beta.div(as.matrix(filt_mpa_table), tree=filt_tree, method="unifrac", weighted=TRUE) + + } else if (opt$metric == "unweighted-unifrac"){ + mat <- rbiom::beta.div(as.matrix(filt_mpa_table), tree=filt_tree, method="unifrac", weighted=FALSE) + } + + } + + # CLR or Aitchison + if (opt$metric == "clr" || opt$metric == "aitchison"){ + # Centered Log-Ratio + ait_norm_mpa_table <- compositions::clr(mpa_table) + mat <- as.matrix(compositions::as.data.frame.rmult(ait_norm_mpa_table)) + + if (opt$metric == "aitchison"){ + # Aitchison + mat <- rbiom::beta.div(mat, method="euclidean", weighted=TRUE) + } + } + + ### Alpha Diversity ### + +} else if (opt$diversity == "alpha"){ + + # Richness + if (opt$metric == "richness"){ + mat <- microbiome::alpha(mpa_table, index = c("richness_observed")) + } + + # Shannon + if (opt$metric == "shannon"){ + mat <- microbiome::alpha(mpa_table, index = c("diversity_shannon")) + } + + # Simpson + if (opt$metric == "simpson"){ + mat <- microbiome::alpha(mpa_table, index = c("diversity_gini_simpson")) + } + + # Gini + if (opt$metric == "gini"){ + mat <- microbiome::alpha(mpa_table, index = c("dominance_gini")) + row.names(mat) <- colnames(mpa_table) + } +} + +write.table(as.matrix(mat), paste0(outfile, '_', opt$metric, '.tsv'), sep = '\t', quote = FALSE) diff --git a/metaphlan/utils/calculate_unifrac.R b/metaphlan/utils/calculate_unifrac.R deleted file mode 100644 index af2b951..0000000 --- a/metaphlan/utils/calculate_unifrac.R +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env Rscript - -args <- commandArgs(trailingOnly = TRUE) - -if(length(args) == 0) -{ - write('Usage: - RScript calculate_unifrac.R - - \tFull path to the merged MetaPhlAn profiles. A table with samples by columns and species by rows is required. - \t\t\tFull path to the MetaPhlAn 3 species Newick tree - \t\t\tBasename for output UniFrac distance matrix - \t\tweighted for Weighted UniFrac, unweighted for Unweighted UniFrac (default weighted) - \t\t\tFunction to apply to the data for normalization. Can be none, sinh_sqrt, log10 (default none) - ', stdout()) - quit(save = 'no') -} - -mpa_infile <- args[1] -tree_file <- args[2] -outfile <- args[3] -weighted <- args[4]=='weighted' || is.na(args[4]) -normalize <- args[5] %in% c('sinh_sqrt','log10') - - -for(x in c(mpa_infile,tree_file)){ -if(!file.exists(x)){ - write(paste0('Input file "', x, '" does not exists! Exiting.'), stdout()) - quit(status = -1) -} -} - -required_pkg <- c('ape','vegan','rbiom') -a <- sapply(required_pkg, function(x) { if (!requireNamespace(x, quietly = TRUE)) - install.packages(x) -}) - - -suppressPackageStartupMessages(library(rbiom)) -suppressPackageStartupMessages(library(vegan)) -suppressPackageStartupMessages(library(ape)) - -mpa_table <- read.table(mpa_infile, comment.char = '#', sep = '\t', header = TRUE) -mpa_table <- mpa_table[grep('s__',mpa_table[,1]),-2] -mpa_table[,1] <- gsub(".+\\|s__", "", mpa_table[,1]) -rownames(mpa_table) <- mpa_table[,1] -mpa_table <- mpa_table[,-1] - -mpa_tree <- ape::read.tree(tree_file) -mpa_tree$tip.label <- gsub(".+\\|s__", "", mpa_tree$tip.label) - -removed <- setdiff(rownames(mpa_table), mpa_tree$tip.label) -if(length(removed)){ - write(paste0('WARNING: ', length(removed), ' species not present in the tree were removed from the input profile.'), stdout()) - write(paste(removed, colllapse='\n'), stdout()) -} -filt_tree <- ape::keep.tip(mpa_tree, intersect(rownames(mpa_table),mpa_tree$tip.label)) -filt_mpa_table <- mpa_table[filt_tree$tip.label,] / 100.0 - -if(normalize == 'log10') - filt_mpa_table <- log10(1 + filt_mpa_table) -if(normalize == 'sinh_sqrt') - filt_mpa_table <- asinh(sqrt(filt_mpa_table)) - -rbiom_distmat <- rbiom::unifrac(as.matrix(filt_mpa_table), weighted=weighted, tree=filt_tree) - -write.table(as.matrix(rbiom_distmat), outfile,sep = '\t', quote = FALSE) \ No newline at end of file diff --git a/metaphlan/utils/external_exec.py b/metaphlan/utils/external_exec.py index 8121fcf..63c5730 100755 --- a/metaphlan/utils/external_exec.py +++ b/metaphlan/utils/external_exec.py @@ -3,7 +3,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import os, sys, re, shutil, tempfile diff --git a/metaphlan/utils/extract_markers.py b/metaphlan/utils/extract_markers.py index 83b732d..2d300f1 100755 --- a/metaphlan/utils/extract_markers.py +++ b/metaphlan/utils/extract_markers.py @@ -4,7 +4,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import sys diff --git a/metaphlan/utils/merge_metaphlan_tables.py b/metaphlan/utils/merge_metaphlan_tables.py index 7b8495a..c7e4aa0 100755 --- a/metaphlan/utils/merge_metaphlan_tables.py +++ b/metaphlan/utils/merge_metaphlan_tables.py @@ -1,86 +1,81 @@ #!/usr/bin/env python3 + import argparse import os import sys -import re import pandas as pd from itertools import takewhile -def merge( aaastrIn, ostm ): + +def merge(aaastrIn, ostm): """ Outputs the table join of the given pre-split string collection. :param aaastrIn: One or more split lines from which data are read. :type aaastrIn: collection of collections of string collections - :param iCol: Data column in which IDs are matched (zero-indexed). - :type iCol: int :param ostm: Output stream to which matched rows are written. :type ostm: output stream """ listmpaVersion = set() - merged_tables = pd.DataFrame() + profiles_list = [] + merged_tables = None for f in aaastrIn: - with open(f) as fin: - headers = [x.strip() for x in takewhile(lambda x: x.startswith('#'), fin)] - if len(headers) == 1: - names = ['clade_name', 'relative_abundance'] - index_col = 0 - if len(headers) >= 4: - names = headers[-1].split('#')[1].strip().split('\t') - index_col = [0,1] + headers = [x.strip() for x in takewhile(lambda x: x.startswith('#'), open(f))] + listmpaVersion.add(headers[0]) - mpaVersion = list(filter(re.compile('#mpa_v[0-9]{2,}_CHOCOPhlAn\w*/{0,3}_[0-9]{0,}').match, headers)) - if len(mpaVersion): - listmpaVersion.add(mpaVersion[0]) + if len(headers) == 4: + names = headers[-1].split('#')[1].strip().split('\t') else: - print('merge_metaphlan_tables found tables without a header including the database version. Exiting.\n') + print('merge_metaphlan_tables: wrong header format for "{}", please check your profiles.\n'.format(f)) return + if len(listmpaVersion) > 1: - print('merge_metaphlan_tables found tables made with different versions of the MetaPhlAn database.\nPlease re-run MetaPhlAn with the same database.\n') + print('merge_metaphlan_tables: profiles from differrent versions of MetaPhlAn, please profile your ' + 'samples using the same MetaPhlAn version.\n') return - - iIn = pd.read_csv(f, - sep='\t', - skiprows=len(headers), - names = names, - usecols=range(3), - ).fillna('') - iIn = iIn.set_index(iIn.columns[index_col].to_list()) - if merged_tables.empty: - merged_tables = iIn.iloc[:,0].rename(os.path.splitext(os.path.basename(f))[0]).to_frame() - else: - merged_tables = pd.merge(iIn.iloc[:,0].rename(os.path.splitext(os.path.basename(f))[0]).to_frame(), - merged_tables, - how='outer', - left_index=True, - right_index=True - ) - if listmpaVersion: - ostm.write(list(listmpaVersion)[0]+'\n') - merged_tables.fillna('0').reset_index().to_csv(ostm, index=False, sep = '\t') -argp = argparse.ArgumentParser( prog = "merge_metaphlan_tables.py", - description = """Performs a table join on one or more metaphlan output files.""") -argp.add_argument( "aistms", metavar = "input.txt", nargs = "+", - help = "One or more tab-delimited text tables to join" ) -argp.add_argument( '-o', metavar = "output.txt", nargs = 1, - help = "Name of output file in which joined tables are saved" ) + iIn = pd.read_csv(f, sep='\t', skiprows=len(headers), names=names, usecols=range(3), index_col=0) + profiles_list.append(pd.Series(data=iIn['relative_abundance'], index=iIn.index, + name=os.path.splitext(os.path.basename(f))[0].replace('_profile', ''))) + + merged_tables = pd.concat([merged_tables, pd.concat(profiles_list, axis=1).fillna(0)], axis=1).fillna(0) + ostm.write(list(listmpaVersion)[0]+'\n') + merged_tables.to_csv(ostm, sep='\t') -__doc__ = "::\n\n\t" + argp.format_help( ).replace( "\n", "\n\t" ) -argp.usage = argp.format_usage()[7:]+"\n\n\tPlease make sure to supply file paths to the files to combine. If combining 3 files (Table1.txt, Table2.txt, and Table3.txt) the call should be:\n\n\t\tpython merge_metaphlan_tables.py Table1.txt Table2.txt Table3.txt > output.txt\n\n\tA wildcard to indicate all .txt files that start with Table can be used as follows:\n\n\t\tpython merge_metaphlan_tables.py Table*.txt > output.txt" +argp = argparse.ArgumentParser(prog="merge_metaphlan_tables.py", + description="Performs a table join on one or more metaphlan output files.") +argp.add_argument("aistms", metavar="input.txt", nargs="*", help="One or more tab-delimited text tables to join") +argp.add_argument("-l", help="Name of file containing the paths to the files to combine") +argp.add_argument('-o', metavar="output.txt", help="Name of output file in which joined tables are saved") +argp.add_argument('--overwrite', default=False, action='store_true', help="Overwrite output file if exists") + +argp.usage = (argp.format_usage() + "\nPlease make sure to supply file paths to the files to combine.\n\n" + + "If combining 3 files (Table1.txt, Table2.txt, and Table3.txt) the call should be:\n" + + " ./merge_metaphlan_tables.py Table1.txt Table2.txt Table3.txt > output.txt\n\n" + + "A wildcard to indicate all .txt files that start with Table can be used as follows:\n" + + " ./merge_metaphlan_tables.py Table*.txt > output.txt") def main( ): - args = argp.parse_args( ) - if args.o is None: - merge(args.aistms, sys.stdout) - else: - with open(args.o[0], 'w') as fout: - merge(args.aistms, fout) + args = argp.parse_args() + + if args.l: + args.aistms = [x.strip().split()[0] for x in open(args.l)] + + if not args.aistms: + print('merge_metaphlan_tables: no inputs to merge!') + return + + if args.o and os.path.exists(args.o) and not args.overwrite: + print('merge_metaphlan_tables: output file "{}" exists, specify the --overwrite param to ovrewrite it!'.format(args.o)) + return + + merge(args.aistms, open(args.o, 'w') if args.o else sys.stdout) + if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk b/metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk deleted file mode 100644 index d5cfc47..0000000 --- a/metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk +++ /dev/null @@ -1 +0,0 @@ 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rmotogae|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__Kosmotoga|s__Kosmotoga_pacifica:0.05702,(GCA_000023325|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__Kosmotoga|s__Kosmotoga_olearia:0.07858,GCA_001636545|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__Kosmotoga|s__Kosmotoga_arenicorallina:0.04537):0.02365):0.02637):0.05672,((GCA_000255135|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Marinitoga|s__Marinitoga_piezophila:0.0533,GCA_900129175|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Marinitoga|s__Marinitoga_hydrogenitolerans:0.03692):0.06104,((GCA_003148465|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Oceanotoga|s__Oceanotoga_teriensis:0.07504,GCA_900102615|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Geotoga|s__Geotoga_petraea:0.07784):0.0522,((GCA_000953715|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Defluviitoga|s__Defluviitoga_tunisiensis:0.07092,GCA_002895485|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_sp_9PWA_NaAc_5_4:0.05144):0.01613,(GCA_000018605|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_mobilis:0.02728,((GCA_002895525|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_olearia:0.03072,GCA_002924625|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_sibirica:0.01435):0.00483,(GCA_002895565|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_mexicana:0.01187,(GCA_002895605|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_miotherma:0.00442,GCA_002924615|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Petrotogales|f__Petrotogales_unclassified|g__Petrotoga|s__Petrotoga_halophila:0.01402):0.00225):0.00734):0.00601):0.0406):0.05723):0.03329):0.05459):0.02128,(GCA_003538775|k__Bacteria|p__Thermotogae|c__Thermotogae_unclassified|o__Thermotogae_unclassified|f__Thermotogae_unclassified|g__Thermotogae_unclassified|s__Thermotogae_bacterium:0.11358,(((GCA_000217815|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga|s__Pseudothermotoga_thermarum:0.05698,(GCA_000017865|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga|s__Pseudothermotoga_lettingae:0.08237,GCA_000816145|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Pseudothermotoga|s__Pseudothermotoga_hypogea:0.06774):0.02339):0.05386,((GCA_000750655|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_neapolitana:0.00893,GCA_002865985|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_sp_SG1:0.00901):0.01788,(GCA_002866025|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_sp_KOL6:0.04374,(GCA_000978555|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_maritima:0.02144,(GCA_000016785|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_petrophila:0.00175,GCA_000025105|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Thermotogaceae|g__Thermotoga|s__Thermotoga_naphthophila:0.00971):0.01691):0.01815):0.00817):0.07558):0.01698,((GCA_003351105|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Thermosipho|s__Thermosipho_africanus:0.03689,(GCA_001990485|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Thermosipho|s__Thermosipho_affectus:0.0361,(GCA_000016905|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Thermosipho|s__Thermosipho_melanesiensis:0.04505,GCA_900129985|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Thermosipho|s__Thermosipho_atlanticus:0.04843):0.02013):0.01132):0.06025,(GCA_001719065|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Fervidobacterium|s__Fervidobacterium_thailandense:0.04431,(GCA_900143265|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Fervidobacterium|s__Fervidobacterium_gondwanense:0.03675,((GCA_000767275|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Fervidobacterium|s__Fervidobacterium_islandicum:0.01805,GCA_900100515|k__Bacteria|p__Thermotogae|c__Thermotogae|o__Thermotogales|f__Fervidobacteriaceae|g__Fervidobacterium|s__Fer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ira|s__Leptospira_haakeii:0.01091,(GCA_002812205|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_neocaledonica:0.00546,GCA_003112675|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_sp_E8:0.00955):0.00388):0.0039):0.00352):0.01657):0.01225):0.01403):0.02105,(GCA_002811955|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_elllisii:0.01315,(GCA_002811985|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_adleri:0.02121,((GCA_000243735|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_kmetyi:0.02556,GCA_002811925|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_barantonii:0.00961):0.00734,((GCA_000243535|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_noguchii:0.01288,(GCA_000243855|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_kirschneri:0.00614,GCA_000347135|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_interrogans:0.00635):0.00752):0.01112,(GCA_000332555|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_alstonii:0.01789,(GCA_001008325|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_santarosai:0.01927,(GCA_000243595|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_weilii:0.01304,(GCA_000013945|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_borgpetersenii:0.01917,(GCA_000243815|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_alexanderi:0.00556,GCA_003429485|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Leptospiraceae|g__Leptospira|s__Leptospira_mayottensis:0.0235):0.00349):0.00323):0.00571):0.00368):0.00533):0.00613):0.00607):0.01031):0.03483):0.03303):0.07465):0.03591):0.03201):0.029,((GCA_000319185|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_pilosicoli:0.02949,(GCA_000431595|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_sp_CAG_700:0.03994,((GCA_000092845|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_murdochii:0.00924,GCA_002379365|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_sp_G79:0.02005):0.01099,(GCA_000316195|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_hampsonii:0.00855,(GCA_001012945|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_hyodysenteriae:0.00969,(GCA_000223215|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_intermedia:0.01163,GCA_001049755|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira|s__Brachyspira_suanatina:0.00361):0.00651):0.01094):0.00402):0.0136):0.01213):0.18812,(((GCA_000568655|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_anserina:0.01949,((GCA_001598195|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_hermsii:0.01987,(GCA_000512145|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_parkeri:0.00417,GCA_003568645|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_turicatae:0.00392):0.00875):0.00481,(GCA_000807295|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_miyamotoi:0.03213,(GCA_000568755|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_coriaceae:0.03416,(GCA_003076595|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borreliella|s__Candidatus_Borrelia_tachyglossi:0.02704,(GCA_000523535|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_duttonii:0.00458,(GCA_000019705|k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Borreliaceae|g__Borrelia|s__Borrelia_recurrentis:0.00211,GCA_00025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othrix|s__Calothrix_sp_NIES_2098:0.03218,(GCA_002218065|k__Bacteria|p__Cyanobacteria|c__Cyanobacteria_unclassified|o__Nostocales|f__Aphanizomenonaceae|g__Nodularia|s__Nodularia_sp_NIES_3585:0.04352,(GCA_002368335|k__Bacteria|p__Cyanobacteria|c__Cyanobacteria_unclassified|o__Nostocales|f__Nostocaceae|g__Nostoc|s__Nostoc_sp_NIES_4103:0.02644,(GCA_000316645|k__Bacteria|p__Cyanobacteria|c__Cyanobacteria_unclassified|o__Nostocales|f__Nostocaceae|g__Nostoc|s__Nostoc_sp_PCC_7524:0.02611,GCA_002896875|k__Bacteria|p__Cyanobacteria|c__Cyanobacteria_unclassified|o__Nostocales|f__Nostocaceae|g__Nostoc|s__Nostoc_sp_CENA543:0.02815):0.00957):0.00475):0.01025):0.01172):0.00718):0.01049):0.00294):0.00434):0.00695):0.00579):0.00658):0.00562):0.00317):0.00998):0.01027):0.00618):0.00552):0.00401):0.00515):0.00998):0.00851):0.00617):0.01287):0.01411):0.0287):0.0491):0.02724):0.01273):0.00689,(((((GCA_002898575|k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__Bacteria_unclassified|s__bacterium_HR17:0.14584,(GCA_002780095|k__Bacteria|p__Armatimonadetes|c__Armatimonadetes_unclassified|o__Armatimonadetes_unclassified|f__Armatimonadetes_unclassified|g__Armatimonadetes_unclassified|s__Armatimonadetes_bacterium_CG07_land_8_20_14_0_80_59_28:0.12368,GCA_002973605|k__Bacteria|p__Abditibacteriota|c__Abditibacteria|o__Abditibacteriales|f__Abitibacteriaceae|g__Abditibacterium|s__Abditibacterium_utsteinense:0.15795):0.01543):0.03164,((GCA_002254585|k__Bacteria|p__Armatimonadetes|c__Armatimonadetes_unclassified|o__Armatimonadetes_unclassified|f__Armatimonadetes_unclassified|g__Armatimonadetes_unclassified|s__Armatimonadetes_bacterium_CP1_7O:0.04873,GCA_002898555|k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__Bacteria_unclassified|s__bacterium_HR15:0.04198):0.08673,(GCA_000427095|k__Bacteria|p__Armatimonadetes|c__Chthonomonadetes|o__Chthonomonadales|f__Chthonomonadaceae|g__Chthonomonas|s__Chthonomonas_calidirosea:0.13093,(GCA_000724625|k__Bacteria|p__Armatimonadetes|c__Fimbriimonadia|o__Fimbriimonadales|f__Fimbriimonadaceae|g__Fimbriimonas|s__Fimbriimonas_ginsengisoli:0.07946,GCA_001898035|k__Bacteria|p__Armatimonadetes|c__Armatimonadetes_unclassified|o__Armatimonadetes_unclassified|f__Armatimonadetes_unclassified|g__Armatimonadetes_unclassified|s__Armatimonadetes_bacterium_55_13:0.08343):0.10462):0.02873):0.03966):0.02639,((((GCA_000092425|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Trueperaceae|g__Truepera|s__Truepera_radiovictrix:0.13602,((GCA_000183745|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Oceanithermus|s__Oceanithermus_profundus:0.09984,GCA_000195335|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Marinithermus|s__Marinithermus_hydrothermalis:0.05693):0.02812,((GCA_000771745|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_filiformis:0.0447,((GCA_900102145|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_arciformis:0.02075,(GCA_000258245|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_thermophilus:0.01334,GCA_001535545|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_parvatiensis:0.01808):0.03437):0.00694,((GCA_000236585|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_sp_CCB_US3_UF1:0.03587,GCA_001399775|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_aquaticus:0.03085):0.01146,(GCA_000309885|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_oshimai:0.03337,(GCA_000187005|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_scotoductus:0.02615,GCA_001880325|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Thermus|s__Thermus_brockianus:0.03368):0.01294):0.00655):0.01628):0.01827):0.04796,(((GCA_000092125|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiothermus_silvanus:0.02589,GCA_003226535|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiothermus_sp_Pnk_1:0.02053):0.03013,(GCA_003574095|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiothermus_roseus:0.03002,GCA_003574345|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiothermus_terrae:0.0278):0.02124):0.0106,((GCA_003351145|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiothermus_sp_QL_1:0.02356,GCA_003574085|k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus|s__Meiotherm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ospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_orleanensis:0.00847,(GCA_001580535|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_cerevisiae:0.01418,GCA_001580695|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_malorum:0.0022):0.01165):0.00383):0.01069,((GCA_000963925|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_cibinongensis:0.01975,GCA_002153685|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_orientalis:0.01705):0.01105,(GCA_002153515|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_indonesiensis:0.02077,(GCA_000755665|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_tropicalis:0.01401,GCA_002156945|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Acetobacter|s__Acetobacter_senegalensis:0.00397):0.01595):0.00951):0.01139):0.00882):0.01679):0.01235):0.00554):0.01692):0.02359):0.01307):0.00747):0.00842):0.04054):0.01147):0.00678):0.00948,((((GCA_000710935|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Alphaproteobacteria_unclassified|f__Alphaproteobacteria_unclassified|g__Alphaproteobacteria_unclassified|s__alpha_proteobacterium_Q_1:0.07258,GCA_900101935|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Kordiimonas|s__Kordiimonas_lacus:0.08495):0.01538,(GCA_002700365|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Kordiimonadales|f__Kordiimonadaceae|g__Kordiimonas|s__Kordiimonas_sp:0.07949,GCA_002740695|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Alphaproteobacteria_unclassified|f__Alphaproteobacteria_unclassified|g__Emcibacter|s__Emcibacter_congregatus:0.0828):0.01887):0.01675,((GCA_002251755|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sandarakinorhabdus|s__Sandarakinorhabdus_cyanobacteriorum:0.05947,(GCA_001295935|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Alphaproteobacteria_unclassified|f__Alphaproteobacteria_unclassified|g__Alphaproteobacteria_unclassified|s__alpha_proteobacterium_AAP81b:0.04084,GCA_002256005|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Alphaproteobacteria_unclassified|f__Alphaproteobacteria_unclassified|g__Alphaproteobacteria_unclassified|s__Alphaproteobacteria_bacterium_PA4:0.03865):0.01399):0.04148,((GCA_003012735|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingosinicella|s__Sphingosinicella_sp_GL_C_18:0.0479,(GCA_900177405|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_indica:0.04354,(GCA_003097155|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_sp_URHD0007:0.09053,GCA_003129465|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingosinicella|s__Sphingosinicella_sp_QZX222:0.05205):0.01541):0.01696):0.02422,(((GCA_000024245|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Zymomonas|s__Zymomonas_mobilis:0.09225,GCA_003385775|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Parasphingopyxis|s__Parasphingopyxis_lamellibrachiae:0.07465):0.02284,((GCA_003050615|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_oleivorans:0.03206,(GCA_900113315|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_jatrophae:0.06904,((GCA_002151445|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_sp_KC8:0.05455,GCA_900188165|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_laterariae:0.03075):0.00886,(GCA_001853345|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_haloaromaticamans:0.04808,GCA_003034225|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_fennica:0.00636):0.0239):0.01563):0.01092):0.00911,(GCA_900101455|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas|s__Sphingomonas_sp_YR710:0.04854,((GCA_000971055|k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomona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roteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Haliea|s__Haliea_salexigens:0.06603):0.00987):0.01182):0.01632,((GCA_000227505|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Halieaceae_unclassified|s__gamma_proteobacterium_HIMB55:0.07232,(GCA_000158175|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Luminiphilus|s__Luminiphilus_syltensis:0.08196,GCA_000169115|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Halieaceae_unclassified|s__marine_gamma_proteobacterium_HTCC2080:0.05363):0.0121):0.02185,(GCA_002868715|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Chromatocurvus|s__Chromatocurvus_sp_F02:0.05515,(GCA_000764025|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Pseudohaliea|s__Pseudohaliea_rubra:0.06461,(GCA_000153125|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Halieaceae|g__Congregibacter|s__Congregibacter_litoralis:0.04981,GCA_000158155|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Gammaproteobacteria_unclassified|f__Gammaproteobacteria_unclassified|g__Gammaproteobacteria_unclassified|s__gamma_proteobacterium_NOR5_3:0.04533):0.03038):0.01211):0.00802):0.01245):0.01014):0.02257):0.01793,(((GCA_002162755|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Gammaproteobacteria_unclassified|f__Gammaproteobacteria_unclassified|g__Gammaproteobacteria_unclassified|s__Gammaproteobacteria_bacterium_50_400_T64:0.02673,GCA_002162815|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Gammaproteobacteria_unclassified|f__Gammaproteobacteria_unclassified|g__Gammaproteobacteria_unclassified|s__Gammaproteobacteria_bacterium_53_120_T64:0.02844):0.06552,(GCA_002707685|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Porticoccaceae|g__Porticoccus|s__Porticoccus_sp:0.06401,(GCA_001438605|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Porticoccaceae|g__Porticoccaceae_unclassified|s__SAR92_bacterium_BACL16_MAG_120619_bin48:0.05987,(GCA_000153445|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Porticoccaceae|g__Porticoccaceae_unclassified|s__gamma_proteobacterium_HTCC2207:0.02928,GCA_000511875|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Porticoccaceae|g__Porticoccaceae_unclassified|s__Gammaproteobacteria_bacterium_MOLA455:0.02118):0.03719):0.04048):0.01239):0.019,(((GCA_000013665|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Saccharophagus|s__Saccharophagus_degradans:0.05448,GCA_000305785|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Simiduia|s__Simiduia_agarivorans:0.09157):0.01874,(GCA_002695945|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Marinimicrobium|s__Marinimicrobium_sp:0.04465,(GCA_002162135|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio_sp_PSBB006:0.03836,(GCA_000019225|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio_japonicus:0.0248,(GCA_003056245|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio_sp_79:0.03301,(GCA_000263355|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio_sp_BR:0.02492,GCA_002268635|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrio|s__Cellvibrio_mixtus:0.03807):0.01445):0.02209):0.01881):0.02477):0.01848):0.01183,(((GCA_000023025|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Teredinibacter|s__Teredinibacter_turnerae:0.06654,GCA_900177435|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadaceae|g__Alteromonadaceae_unclassified|s__Alteromonadaceae_bacterium_Bs31:0.05458):0.03757,(GCA_002707785|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Cellvibrionaceae_unclassified|s__Cellvibrionaceae_bacterium:0.06462,(GCA_000209515|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Alteromonadales_unclassified|g__Alteromonadales_unclassified|s__gamma_proteobacterium_IMCC1989:0.07311,GCA_001723645|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Cellvibrionaceae|g__Candidatus_Endobugula|s__Candidatus_Endobugula_sertula:0.07361):0.02825):0.01285):0.01447,((GCA_001750105|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Cellvibrionales|f__Microbulbiferaceae|g__Microbulbifer|s__Microbulbifer_aggregans:0.05181,GCA_003076275|k__Bacteria|p__Proteobacteria|c__Gammapr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obacterales|f__Yersiniaceae|g__Yersiniaceae_unclassified|s__Yersiniaceae_bacterium_2016Iso4:0.01599,(GCA_002858675|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersiniaceae_unclassified|s__Yersiniaceae_bacterium_2015Iso6:0.01123,GCA_002858805|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersiniaceae_unclassified|s__Yersiniaceae_bacterium_2016Iso3:0.01447):0.00348):0.02632):0.01122):0.00793,((GCA_002082115|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_nematodiphila:0.02459,((GCA_000988045|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_ureilytica:0.03111,GCA_002206385|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_odorifera:0.0314):0.01719,(GCA_900456935|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_grimesii:0.01347,(GCA_900187015|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_ficaria:0.00249,GCA_900478125|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_plymuthica:0.02639):0.0076):0.04216):0.01947):0.01471,(GCA_001422575|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_sp_Leaf51:0.02338,(GCA_002834385|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella_sp_AA:0.02403,(GCA_002303785|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella_victoriana:0.03772,((GCA_002951615|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella_sp_ERMR1_05:0.03119,GCA_003573465|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rahnella|s__Rahnella_aquatilis:0.03385):0.02105,((GCA_000520015|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Chania|s__Chania_multitudinisentens:0.04306,(GCA_002291425|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Gibbsiella|s__Gibbsiella_quercinecans:0.03208,GCA_900451015|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Ewingella|s__Ewingella_americana:0.06089):0.02071):0.00799,(GCA_900457075|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_quinivorans:0.0182,(GCA_002588845|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_fonticola:0.02956,GCA_003146705|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_marcescens:0.0532):0.01153):0.01047):0.0178):0.01065):0.01598):0.01647):0.01801):0.01179):0.01307,(((GCA_003097335|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_sp_S1B:0.09486,(GCA_000496755|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_sp_DD3:0.03732,(GCA_001976145|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_oryzae:0.02915,(GCA_003524615|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_liquefaciens:0.02377,GCA_900175135|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_proteamaculans:0.01454):0.02164):0.01602):0.00549):0.01793,((GCA_002093665|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella|s__Rouxiella_badensis:0.0256,(GCA_000257645|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia_sp_M24T3:0.02281,GCA_002093625|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Rouxiella|s__Rouxiella_silvae:0.03199):0.01227):0.02649,((GCA_000582515|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia_similis:0.0317,(GCA_003010765|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia_pseudotuberculosis:0.0054,(GCA_000268985|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia_pestis:0.00724,GCA_001319825|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Yersinia|s__Yersinia_wautersii:0.00492):0.00608):0.01447):0.01078,(((GCA_001319845|k__Bacter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ella|s__Raoultella_ornithinolytica:0.01528):0.01581):0.01883,(GCA_000757785|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Pluralibacter|s__Pluralibacter_gergoviae:0.05163,((GCA_002393445|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea_neteri:0.03758,GCA_900446735|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea_davisae:0.04067):0.04237,((GCA_000262305|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia|s__Shimwellia_blattae:0.04559,GCA_000512125|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_albertii:0.02891):0.01802,(GCA_001022135|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacterales_unclassified|g__Phytobacter|s__Phytobacter_ursingii:0.01031,GCA_001856865|k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Metakosakonia|s__Kluyvera_intestini:0.01864):0.013):0.00918):0.00822):0.00657):0.02137):0.00977):0.00518):0.01652):0.00889):0.00698):0.00903):0.00619):0.01329):0.00683):0.01087):0.00919):0.00519):0.0053):0.00965):0.0236):0.01368):0.00939):0.01148):0.00606):0.01197):0.01562):0.00757):0.008):0.0054):0.00955):0.00942):0.01481):0.015):0.02125):0.01139):0.00884):0.00877):0.01371):0.01026):0.00809):0.03069):0.01722):0.00968):0.00584):0.00511):0.00557):0.0073):0.00266):0.00357):0.01008):0.00806):0.01018):0.01143):0.01137):0.01067):0.01128):0.00771):0.0074):0.00716):0.00464):0.00456):0.0103):0.05891):0.032275); \ No newline at end of file diff --git a/metaphlan/utils/mpa_v4beta_Jan21_SGB_tree.nwk b/metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103.nwk similarity index 100% rename from metaphlan/utils/mpa_v4beta_Jan21_SGB_tree.nwk rename to metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103.nwk diff --git a/metaphlan/utils/Jan21_SGB2GTDB.tsv b/metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv similarity index 100% rename from metaphlan/utils/Jan21_SGB2GTDB.tsv rename to metaphlan/utils/mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv diff --git a/metaphlan/utils/parallelisation.py b/metaphlan/utils/parallelisation.py index 2b3635b..e3eb9f2 100755 --- a/metaphlan/utils/parallelisation.py +++ b/metaphlan/utils/parallelisation.py @@ -3,7 +3,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' try: diff --git a/metaphlan/utils/plot_tree_graphlan.py b/metaphlan/utils/plot_tree_graphlan.py index 77bc1e9..0911e48 100755 --- a/metaphlan/utils/plot_tree_graphlan.py +++ b/metaphlan/utils/plot_tree_graphlan.py @@ -1,7 +1,7 @@ #!/usr/bin/env python __author__ = ('Duy Tin Truong (duytin.truong@unitn.it), ' 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import argparse as ap diff --git a/metaphlan/utils/sample2markers.py b/metaphlan/utils/sample2markers.py index 18ca447..3ab8c84 100755 --- a/metaphlan/utils/sample2markers.py +++ b/metaphlan/utils/sample2markers.py @@ -4,7 +4,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import sys diff --git a/metaphlan/utils/sgb_to_gtdb_profile.py b/metaphlan/utils/sgb_to_gtdb_profile.py index 94fdbc8..3512444 100755 --- a/metaphlan/utils/sgb_to_gtdb_profile.py +++ b/metaphlan/utils/sgb_to_gtdb_profile.py @@ -1,3 +1,7 @@ +__author__ = 'Aitor Blanco (aitor.blancomiguez@unitn.it' +__version__ = '4.0.0' +__date__ = '22 Aug 2022' + import os, time, sys import argparse as ap @@ -6,7 +10,7 @@ except ImportError: from util_fun import openw, info, error -GTDB_ASSIGNMENT_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), "Jan21_SGB2GTDB.tsv") +GTDB_ASSIGNMENT_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), "mpa_vJan21_CHOCOPhlAnSGB_202103_SGB2GTDB.tsv") def read_params(): p = ap.ArgumentParser(description="", formatter_class=ap.ArgumentDefaultsHelpFormatter) diff --git a/metaphlan/utils/strain_transmission.py b/metaphlan/utils/strain_transmission.py index 790a8b6..c6ccda1 100755 --- a/metaphlan/utils/strain_transmission.py +++ b/metaphlan/utils/strain_transmission.py @@ -1,6 +1,6 @@ __author__ = ('Aitor Blanco (aitor.blancomiguez@unitn.it), ' 'Mireia Valles-Colomer (mireia.vallescolomer@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' import os, time, sys diff --git a/metaphlan/utils/util_fun.py b/metaphlan/utils/util_fun.py index 31fa720..7bbc4a8 100755 --- a/metaphlan/utils/util_fun.py +++ b/metaphlan/utils/util_fun.py @@ -3,7 +3,7 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__version__ = '4.beta.3' +__version__ = '4.0.0' __date__ = '22 Aug 2022' diff --git a/setup.py b/setup.py index 41a4686..bf393e9 100755 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ setuptools.setup( name='MetaPhlAn', - version='4.beta.3', + version='4.0.0', author='Aitor Blanco-Miguez', author_email='aitor.blancomiguez@unitn.it', url='http://github.com/biobakery/MetaPhlAn/',