fDOG tool is distributed as a python package called fdog. It is compatible with Python ≥ v3.7.
You can install fdog using pip:
python3 -m pip install fdog
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 fdog
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
After installing fdog, you need to setup fdog to get its dependencies and pre-calculated data.
NOTE: in case you haven't installed greedyFAS, it will be installed automatically within fDOG setup. However, you need to run setupFAS after fDOG setup finished before actually using fDOG!
You can setup fDOG by running this command
fdog.setup -d /output/path/for/fdog/data
Pre-calculated data set of fdog will be saved in /output/path/for/fdog/data. After the setup run successfully, you can start using fdog. Please make sure to check if you need to run setupFAS first.
You will get a warning if any of the dependencies are not ready to use, please solve those issues and rerun fdog.setup.
For debugging the setup, please create a log file by running the setup as e.g. fdog.setup | tee log.txt and send us that log file, so that we can trouble shoot the issues. Most of the problems can be solved by just re-running the setup.
fdog will run smoothly with the provided sample input file 'infile.fa' if everything is set correctly.
fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3
The output files with the prefix test will be saved at your current working directory.
You can have an overview about all available options with the command
fdog.run -h
Please find more information in our wiki to learn about the input and outputs files of fdog.
Within the data package we provide a set of 78 reference taxa. They can be automatically downloaded during the setup. This data comes "ready to use" with the fdog framework. Species data must be present in the three directories listed below:
- searchTaxa_dir (Contains sub-directories for proteome fasta files for each species)
- coreTaxa_dir (Contains sub-directories for BLAST databases made with
makeblastdbout of your proteomes) - annotation_dir (Contains feature annotation files for each proteome)
For each species/taxon there is a sub-directory named in accordance to the naming schema ([Species acronym]@[NCBI ID]@[Proteome version])
fdog is not limited to those 78 taxa. If needed the user can manually add further gene sets (multiple fasta format) using provided functions.
For adding one gene set, please use the fdog.addTaxon function:
fdog.addTaxon -f newTaxon.fa -i tax_id [-o /output/directory] [-n abbr_tax_name] [-c] [-v protein_version] [-a]
in which, the first 3 arguments are required including newTaxon.fa is the gene set that need to be added, tax_id is its NCBI taxonomy ID, /output/directory is where the sub-directories can be found (genome_dir, blast_dir and weight_dir). If not given, new taxon will be added into the same directory of pre-calculated data. Other arguments are optional, which are -n for specify your own taxon name (if not given, an abbriviate name will be suggested based on the NCBI taxon name of the input tax_id), -c for calculating the BLAST DB (only needed if you need to include your new taxon into the list of taxa for compilating the core set), -v for identifying the genome/proteome version (default will be the current date ), and -a for turning off the annotation step (not recommended).
For adding more than one gene set, please use the fdog.addTaxa script:
fdog.addTaxa -i /path/to/newtaxa/fasta -m mapping_file [-o /output/directory] [-c]
in which, /path/to/taxa/fasta is a folder where the FASTA files of all new taxa can be found. mapping_file is a tab-delimited text file, where you provide the taxonomy IDs that stick with the FASTA files:
#filename tax_id abbr_tax_name version
filename1.fa 12345678
filename2.faa 9606
filename3.fasta 4932 my_fungi
...
The header line (started with #) is a Must. The values of the last 2 columns (abbr. taxon name and genome version) are, however, optional. If you want to specify a new version for a genome, you need to define also the abbr. taxon name, so that the genome version is always at the 4th column in the mapping file.
NOTE: After adding new taxa into fdog, you should check for the validity of the new data before running fdog.
Any bug reports or comments, suggestions are highly appreciated. Please open an issue on GitHub or be in touch via email.
Ebersberger, I., Strauss, S. & von Haeseler, A. HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 9, 157 (2009), doi:10.1186/1471-2148-9-157
For further support or bug reports please contact: [email protected]