dcc2 0.3.3

Dynamic core ortholog compilation tool

dcc2

dcc2 is a tool for compiling core set data for fDOG using predicted orthologs from OMA (either OMA-browser or OMA-standalone), as well as from an OrthoXML file resulted from any ortholog search tools.

Outputs of this tool are 3 (optional 4) folders required for a fDOG run, including (1) core_orthologs, where a multiple fasta file and a corresponding profile HMM can be found, (2) genome_dir contains gene sets of taxa, from which the orthologs are originated, (3) blast_dir holds the blast databases of those gene sets within genome_dir, and an optional (4) weight_dir that contains feature architecure annotations of all gene sets.

Table of Contents

• How to install
  • Install the dcc2 package
  • Setup dcc2
• Usage
• Bugs
• Contributors
• Contact

How to install

dcc2 is distributed as a python package called dcc2. It is compatible with Python ≥ v3.7.

Install the dcc2 package

You can install dcc2 using pip:

python3 -m pip install dcc2

or, in case you do not have admin rights, and don't use package systems like Anaconda to manage environments you need to use the --user option:

python3 -m pip install --user dcc2

and then add the following line to the end of your ~/.bashrc or ~/.bash_profile file, restart the current terminal to apply the change (or type source ~/.bashrc):

export PATH=$HOME/.local/bin:$PATH

Setup dcc2

After installing dcc2, you need to run the prepare script to download and parse required OMA browser data.

You can do it by running this command

dcc.prepare -o /output/path/for/oma/data

Usage

For parsing OMA orthologs by using an OMA group ID:

dcc.parseOmaById -g 1 -n HUMAN,THEAM,DESM0 -o /output/path/ -j jobName --cpus 8

Or using list of OMA taxa:

dcc.parseOmaBySpec -n HUMAN,ECOLI,YEAST -o /output/path/ -j jobName --annoFas --cpus 8 [--missingTaxa 1]

--missingTaxa deinfies the number of taxa that are allowed to be absent in each ortholog group.

If only 2 OMA taxa are given, you can choose to use OMA pairs instead of OMA groups:

dcc.parseOmaBySpec -n HUMAN,ECOLI -t pair -o /output/path/ -j jobName --annoFAS --cpus 8

For parsing an output from OMA-standalone or an OrthoXML file, dcc2 requires:

• the output orthoXML file of the ortholog groups,
• a taxon mapping file in tab-delimited format containing 3 columns <NCBI taxon ID> <Original taxon name> <Abbr. taxon name>, where original taxon name is the name that is written in the orthoXML input file and abbr. taxon name is its abbreviation species code (for example: HOMSA for Homo sapiens)
• protein set of included taxa. In case of OMA, this can be either given as a folder, or automatically downloaded from OMA database

dcc.parseOrthoxml -i input.orthoxml -m mapping_file.txt -g /path/to/gene/set -o /output/path/ -j jobName --annoFas --cpus 8

One can also limit the taxa included in the ortholog groups, if not all the taxa in the orthoXML file are needed. In this case, just reduce the taxon mapping file to contain only required taxa and use this function:

dcc.parseOrthoxmlCustom -i input.orthoxml -m mapping_file_reduced.txt -g /path/to/gene/set -o /output/path/ -j jobName --annoFas --cpus 8 [--minTaxa 10]

--minTaxa defines the minimum number of taxa should be included in each ortholog group.

Bugs

Any bug reports or comments, suggestions are highly appreciated. Please open an issue on GitHub or be in touch via email.

Contributors

• Vinh Tran
• Hannah Mülbaier

Contact

For further support or bug reports please contact: [e-mail]