trvinh/fcat_r

fCAT

Installation

To install fCAT, open R in your terminal

Using devtools to install fCAT

if (!requireNamespace("devtools"))
    install.packages("devtools")
devtools::install_github("giangnguyen0709/fCAT")

Usage

checkCompleteness

The function to check the completeness of an interested genome

• genome: The path to the genome fasta file. The name of the fasta file must be SPECIES@ncbiID@version, for example: HUMAN@9606@3
• fasAnno: The path to the fas annotation file (must has the same name as the genome fasta file). It can equal NULL. If fasAnno equal NULL, fCAT will compute the FAS annotation for the genome fasta file.
• coreDir: The path to the core directory, where the core set is stored within weight_dir, blast_dir, etc.
• coreSet: The name of the interested core set. The core directory can contains more than one core set and the user must specify the interested core set. The core set will be stored in the folder core_orthologs in subfolder, specify them by the name of the subfolder
• extend: Optional, by default is FALSE. The output of the function is a phylogenetic profile of the interested genome. It contains 4 files, .phyloprofile, .extended.fa, _reverse.domains and _forward.domains. If extend = TRUE, the files will be appended into the old files in the folder output of the core directory or in the inputed folder by the user with the argument ppDir. If there is no old files in the folder, the output files of the function will be writen in the new files.
• redo: Optional, by default is FALSE. If it exists already the genome ID of the interested genome in the old phylogenetic profile. The tool will extract direct this pp to assess the completeness. If user don't want this happens, they can set redo to TRUE to get a new phylogenetic profile
• scoreMode: the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"
• priorityList: A list contains one or many genome ID of the genomes, which were used to build the core set. The genome ID of this list will be stored with an priority order, the tool look at into the fasta file of each core group and uses the priority order to determine the references species for each core group.
• cpu: Optional, by default is 4. determines the cores that fDOG and fdogFAS will uses to be run parallel
• blastDir: Optional. The user can replace the blast_dir folder in the core directory by specifying it in this argument. By default is NULL
• weightDir: Optional. The user can replace the weight_dir folder in the core directory by specifying it in this argument. By default is NULL
• outDir: Optional. The user can specify the directory to save the output report file of the completeness of the interested genome by specifying the path to the folder in this argument. By default is NULL
• cleanup: Optional, by default is FALSE. The fDOG's output is a set of phylogenetic profile of each core group to the interested genome. The phylogenetic profile will be stored into a folder in the core set. The function will merge all the small phylogenetic profile, calculate the FAS score or length to have the whole phylogenetic profile of the interested genome to the core set. This fDOG's output can be reused for all score modes. When cleanup is set to TRUE, the fDOG's output will not be stored to be reused but to be removed
• reFdog: Optional, by default is FALSE. If it already exist a fDOG's output for a specific core group the tool will skip this core group and go to the next core group. If reFdog is set to TRUE, the tool will remove all the existed fDOG's output and rerun fDOG for all core groups of the set
• fdogDir: Optional, by default is NULL. Normally the fDOG's output will be stored in the folder fdogout in the core directory, but the user can specify the folder for fDOG's output by specify the path to it in this argument. Notice here, is that the fDOG's output folder will contains the subfolder, equivalent to the name of the interested genome, for example, the folder can contain "HUMAN@9606@3" and "AMPQU@400682@2", for a completeness checking on an interested genome, which has a subfolder in the fDOG's output folder with the same name, the function will look into the subfolder to find the existed fDOG's output
• ppDir: Optional. The user can replace the default folder output in the core directory, where the phylogenetic profiles are stored by his folder. The user can specify the path to his folder in this argument. By default is NULL

The function returns two reports. A detailed report of the completeness of the interested genome and a frequency table of all taxa, which were checked completeness with fCAT with option extend = TRUE. The frequency table show how many core genes "similar", "dissimilar", "duplicated", "missing" and "ignored" in each taxon.

genome <- "/path/to/query/genome.fa"
fasAnno <- "/path/to/fas/annotation/genome.json"
coreDir <- "/path/to/the/core/directory"
coreSet <- "name of the core set"
extend <- TRUE #by default is FALSE
redo <- TRUE #by default is FALSE
scoreMode <- 2 #Choices: 1,2,3, "busco"
priorityList <- c("HUMAN@9606@1", "ECOLI@511145@1") 
cpu <- 4
blastDir <- "/path/to/blast_dir" #Optional
weightDir <- "/path/to/weight_dir" #Optional
outDir <- "/path/to/the/output/folder" #By default the report files will be stored in the core directory
cleanup <- TRUE #by default is FASLE
reFdog <- TRUE #by default is FALSE
fdogDir <- "/path/to/the/folder/to/store/fdog/output" #Optional
ppDir <- "/path/to/the/folder/to/store/the/phylogenetic/profile"

checkCompleteness <- function(genome, fasAnno, coreDir, coreSet, extend, redo, scoreMode, priorityList, cpu, blastDir, weightDir, outDir, cleanup, reFdog, fdogDir, ppDir)

computeOriginal

The function to compute the original phylogenetic profile, which will contains the phylogenetic profile of all core taxa of the core set. This phylogenetic profile can be used to assess the completeness of the core taxa and their'completeness will be reported together with the interested genome in the frequency table. It is optional, the tool can still check the completeness of a genome, even the orginal phylogenetic profile was not computed

• coreDir: The path to the core directory, where the core set is stored within weight_dir, blast_dir, etc.
• coreSet: The name of the interested core set. The core directory can contains more than one core set and the user must specify the interested core set. The core set will be stored in the folder core_orthologs in subfolder, specify them by the name of the subfolder
• scoreMode: the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"
• cpu: Optional, by default is 4. Determines the cores that fDOG and fdogFAS will uses to be run parallel
• cleanup: Optional, by default is FALSE. The fDOG's output is a set of phylogenetic profile of each core group to the interested genome. The phylogenetic profile will be stored into a folder in the core set. The function will merge all the small phylogenetic profile, calculate the FAS score or length to have the whole phylogenetic profile of the interested genome to the core set. This fDOG's output can be reused for all score modes. When cleanup is set to TRUE, the fDOG's output will not be stored to be reused but to be removed
• ppDir: Optional, by default is NULL. The user can replace the default folder output in the core directory, where the phylogenetic profiles are stored by his folder. The user can specify the path to his folder in this argument

This funtion will append the orginal phylogenetic profile of the core taxa in to the existing phylogenetic profile in folder output by default or in folder phyloprofile, which was directed by the user with the argument ppDir

coreDir <- "/path/to/the/core/directory"
coreSet <- "name of the core set"
scoreMode <- 2 #Choices: 1,2,3, "busco"
cpu <- 4
cleanup <- TRUE #by default is FASLE
ppDir <- "/path/to/the/folder/to/store/the/phylogenetic/profile"

fCAT::computeOriginal(coreDir, coreSet, scoreMode, cpu, cleanup, ppDir)

processCoreSet

The function calculate all cutoff values for all mode in the set. For score mode 1 it will calculate the avarage of all vs all FAS scores between the training sequences in the core gene. For score mode 2 it will calculate the avarage of the FAS score between each sequence against all training sequences in the core gene. The scores will be writen in a table with a column is the ID of the sequences and a column is the corresponding value. For score mode 3, the function will calculate the avarage of 1 vs all FAS scores for each training sequence in the core gene. The avarages build a distribution, the function will calculate the confidence interval of this distribution and write the upper value and the lower value of the interval in a file in the core gene folder.

• coreDir: The path to the core directory, where the core set is stored within weight_dir, blast_dir, etc.
• coreSet: The name of the interested core set. The core directory can contains more than one core set and the user must specify the interested core set. The core set will be stored in the folder core_orthologs in subfolder, specify them by the name of the subfolder

coreDir <- "/path/to/the/core/directory"
coreSet <- "name of the core set"

fCAT::processCoreSet(coreDir, coreSet)

Examples

The test data is the eukaryota_busco set, which can be downloaded in https://applbio.biologie.uni-frankfurt.de/download/core-sets/BUSCO_Eukaryota/

The core set folder has some conflicts with the input of fCAT, which must be removed first. All the core gene folders in the folder core_orthologs must be contained in a subfolder (The name of the subfolder is the core set argument of fCAT) and this subfolder must be stored in core orthologs. In this document I will set the name of this subfolder eukaryota_busco. In the blast dir folder of CRYNE, the symbolic link of the fasta file of CRYNE was directed by a mistake to the symbolic link of CHRLE. This must be corrected before testing

The folder weight_dir of the core set contains the the xml files, which can not be run with fCAT. Please download the annotation files of the core set from https://drive.google.com/file/d/113MBwT1n7E64Xk54Ul-_r82aEK2v8jdl/view?usp=sharing and replace the xml files with the json files

In all following examples, I assumed that I has a genome fasta file and its FAS annotation file, which named HUMAN@[email protected] and HUMAN@[email protected], the core folder named eukaryota_busco, the core set named eukaryota_busco and all this data is placed in the home folder. You can replace them by your corresponding path and names

genome <- "/home/user/HUMAN@[email protected]"
fasAnno <- "/home/user/HUMAN@[email protected]"
coreDir <- "/home/user/eukaryota_busco"
coreSet <- "eukaryota_busco"
extend <- TRUE
priorityList <- c("HOMSA@9606@2")
scoreMode <- 1
cpu <- 4

fCAT::checkCompleteness(genome = genome, fasAnno = fasAnno, coreDir = coreDir, coreSet = coreSet, extend = extend, priorityList = priorityList, scoreMode = scoreMode, cpu = cpu)

The report will be storede by default in /home/user/eukaryota_busco/output/eukaryota_busco/1/report

coreDir <- "/home/user/eukaryota_busco"
coreSet <- "eukaryota_busco"
scoreMode <- 1
cpu <- 4

fCAT::computeOriginal(coreDir = coreDir, coreSet = coreSet, scoreMode = scoreMode, cpu = cpu)

The phylogenetic profile of all core taxa will be computed and be stored by default in /home/user/eukaryota_busco/output/eukaryota_busco/1

coreDir <- "/home/user/eukaryota_busco"
coreSet <- "eukaryota_busco"

fCAT::processCoreSet(coreDir = coreDir, coreSet = coreSet)

The function will calculate all cutoff values for all core genes in the set and write them in a text file, which will be stored in /home/user/eukaryota_busco/core_orthologs/eukaryota_busco/core_gene/fas_dir/score_dir

Depencies

fCAT is depended on some tools.

fDOG

https://github.com/BIONF/fDOG

FAS

https://github.com/BIONF/FAS

Packages in R

R.utils

taxize

EnvStats