In this repository I provide the taxonomy information of different mOTUs version, ready to be loaded into R.

mOTUs 3.0

To load the taxonomy of the mOTUs for the database version 3.0.0 and 3.0.1 you can use:

load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_taxonomy_3.0.1.Rdata?raw=true"))

mOTUs 2.6

To load the taxonomy of the mOTUs for the database version 2.6.0 and 2.6.1 you can use:

load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_taxonomy_2.6.1.Rdata?raw=true"))

mOTUs 2.5

To load the taxonomy of the mOTUs for the database version 2.5.0 and 2.5.1 you can use:

load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_taxonomy_2.5.1.Rdata?raw=true"))

Useful functions

Additionally I provide two functions that can be loaded with:

load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_functions.Rdata?raw=true"))

There are two functions:

extract_motus_id

Which given the name of a profiled mOTUs, it extract the mOTUs ID. Example input: "Abiotrophia defectiva [ref_mOTU_v25_04788]" and output: "ref_mOTU_v25_04788"

motus_summarise_higher_level

Which given a taxonomic profile table, it can summarise the profile at higher taxonomic level. The input are:

• profile, the mOTUs taxonomic profile. expect to have rownames as mOTUs and colnames as samples
• taxonomy, the mOTUs taxonomy. as downloaded from any of the command listed before
• level, the taxonomic level to which you want to change the taxonomic profile
• convert_NA, convert NAs to -1. For example "NA Clostria unknown genus" and "NA Firmicutes unknown genus" would both be added to unassigned. By default this is set to True.

Example command:

# we load the functions
load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_functions.Rdata?raw=true"))
# we load a table of samples: 2,010 samples profiled with mOTUs 2.5.1
load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/example_healthy_human_gut.Rdata?raw=true"))
# we load the taxonomy information for mOTUs 2.5
load(url("https://github.com/AlessioMilanese/motus_taxonomy/blob/master/data/motus_taxonomy_2.5.1.Rdata?raw=true"))

# we convert the taxonomic table from species level to genus:
genus_table = motus_summarise_higher_level(PROFILES,motus2.5_taxonomy,"Genus")

How to load a mOTUs table into R

Let's say you run:

motus merge -i sample1.motus,sample2.motus -o ~/Desktop/merged.motus

on the terminal and obtain a motus table in ~/Desktop/merged.motus which look like:

head ~/Desktop/merged.motus
  # motus version 2.5.1 | merge 2.5.1 | info merged profiles: # git tag version 2.5.1 |  motus version 2.5.1 | map_tax 2.5.1 | gene database: nr2.5.1 | calc_mgc 2.5.1 -y insert.scaled_counts -l 75 | calc_motu 2.5.1 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_2.5.1 meta_mOTU_2.5.1 
  # call: python motus merge -i sample1.motus,sample2.motus -o ~/Desktop/merged.motus
  #consensus_taxonomy	sample1	sample2
  Leptospira alexanderi [ref_mOTU_v25_00001]	0.0000000000	0.0000000000
  Leptospira weilii [ref_mOTU_v25_00002]	0.0000000000	0.0000000000
  Chryseobacterium sp. [ref_mOTU_v25_00004]	0.0000000000	0.0000000000
  Chryseobacterium gallinarum [ref_mOTU_v25_00005]	0.0000000000	0.0000000000
  Chryseobacterium indologenes [ref_mOTU_v25_00006]	0.0000000000	0.0000000000
  Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v25_00007]	0.0000000000	0.0000000000
  Chryseobacterium jejuense [ref_mOTU_v25_00008]	0.0000000000	0.0000000000

In R, you can load it with:

merged_motus = read.csv("~/Desktop/merged.motus",header = T, sep = "\t", row.names = 1, skip = 2, check.names = F)