Package: fdog
fDOG - Feature-aware Directed OrtholoG searchTable of ContentsHow to installInstall the fDOG packageSetup fDOGUsagefDOG data setAdding a new gene set into fDOGAdding a list of gene sets into fDOGBugsHow to citeContributorsContactHow to installfDOGtool is distributed as a python package calledfdog. It is compatible withPython ≥ v3.7.Install the fDOG packageYou can installfdogusingpip:python3 -m pip install fdogor, in case you do not have admin rights, and don't use package systems like Anaconda to manage environments you need to use the--useroption:python3 -m pip install --user fdogand then add the following line to the end of your~/.bashrcor~/.bash_profilefile, restart the current terminal to apply the change (or typesource ~/.bashrc):export PATH=$HOME/.local/bin:$PATHSetup fDOGAfter installingfdog, you need to setupfdogto get its dependencies and pre-calculated data.NOTE: in case you haven't installedgreedyFAS, it will be installed automatically withinfDOGsetup. However, you need to runsetupFASafterfDOGsetup finished before actually usingfDOG!You can setup fDOG by running this commandfdog.setup -d /output/path/for/fdog/dataPre-calculated data setof fdog will be saved in/output/path/for/fdog/data. After the setup run successfully, you can start usingfdog.Please make sure to check if you need to runsetupFASfirst.You will get a warning if any of the dependencies are not ready to use, please solve those issues and rerunfdog.setup.For debugging the setup, please create a log file by running the setup as e.g.fdog.setup | tee log.txtand 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.Usagefdogwill 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@3The output files with the prefixtestwill be saved at your current working directory.
You can have an overview about all available options with the commandfdog.run -hPlease find more information inour wikito learn about theinput and outputs filesoffdog.fDOG data setWithin 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 thefdogframework. 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 withmakeblastdbout 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])fdogis not limited to those 78 taxa. If needed the user can manually add further gene sets (multiple fasta format) using provided functions.Adding a new gene set into fDOGFor addingone gene set, please use thefdog.addTaxonfunction: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 includingnewTaxon.fais the gene set that need to be added,tax_idis its NCBI taxonomy ID,/output/directoryis where the sub-directories can be found (genome_dir,blast_dirandweight_dir). If not given, new taxon will be added into the same directory of pre-calculated data. Other arguments are optional, which are-nfor specify your own taxon name (if not given, an abbriviate name will be suggested based on the NCBI taxon name of the inputtax_id),-cfor calculating the BLAST DB (only needed if you need to include your new taxon into the list of taxa for compilating the core set),-vfor identifying the genome/proteome version (default will be the current date ), and-afor turning off the annotation step (not recommended).Adding a list of gene sets into fDOGFor addingmore than one gene set, please use thefdog.addTaxascript:fdog.addTaxa -i /path/to/newtaxa/fasta -m mapping_file [-o /output/directory] [-c]in which,/path/to/taxa/fastais a folder where the FASTA files of all new taxa can be found.mapping_fileis 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 intofdog, you shouldcheck for the validity of the new databefore running fdog.BugsAny bug reports or comments, suggestions are highly appreciated. Pleaseopen an issue on GitHubor be in touch via email.How to citeEbersberger, I., Strauss, S. & von Haeseler, A. HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 9, 157 (2009),doi:10.1186/1471-2148-9-157ContributorsIngo EbersbergerVinh TranHolger BergmannContactFor further support or bug reports please contact:ebersberger@bio.uni-frankfurt.de