Package: omamo
OMAMO: orthology-based model organism selectionOMAMO is a tool that suggests the best model organism to study a biological process based on orthologous relationship between a species and human.The user can consider several species as potential model organisms and the algorithm will rank them and report the output for a given biological process (searched as a GO term or a GO ID) is produced in the dataframe format.DependenciesFollowing Python packages are needed: numpy, matplotlib, pickle and pandas. Besides, you need to installpyOMA.PipelineFirstly, download the OMA dataset:wget  https://omabrowser.org/All/OmaServer.h5  -O data/OmaServer.h5  #caution: 94GBSecondly, using the filedata/oma-species.txtfind the five-letter UniProt code for species of interest. For example, consider three speciesDicdyostelium discodeium,Neurospora crassaandSchizosaccharomyces pombe. Their UniProt codes areDICDI,NEUCRandSCHPO, respectively.Install omamo from the git checkout:pipinstall<path_to_omamo.git>Once the package is installed, you should be able to runomamoas a command. Withomamo -hsee the available options:usage: omamo [-h] --db DB [--query QUERY] [--ic IC] [--h5-out H5_OUT] [--tsv-out TSV_OUT] --models MODELS [MODELS ...]

Run omamo for a set of model organisms

optional arguments:
  -h, --help            show this help message and exit
  --db DB               Path to the HDF5 database
  --query QUERY         Name of the Query species, defaults to HUMAN
  --ic IC               Path to the information content file (tsv format)
  --h5-out H5_OUT       Path to the HDF5 output file. If omitted, not stored in this format
  --tsv-out TSV_OUT     Path to the TSV output file. If omitted, not stored in this format
  --models MODELS [MODELS ...]
                        List of model species, or a path to a txt file with the model speciesIn order to create the omamo data forDicdyostelium discodeium,Neurospora crassaandSchizosaccharomyces pombe,
we would run omamo with the following parameters:omamo --db OmaServer.h5 --query HUMAN --tsv-out omamo_output_df.csv --models  DICDI NEUCR SCHPOYou might face an error aboutOSError: ``OmaServer.h5.idx`` does not existandpyoma.browser.db.DBConsistencyError: Suffix index for protein sequences is not availablewhich you can ignore them.Finally, the output data frame is ready as a TSV fileomamo_output_df.csv. For example, for the GO ID ofGO0000472, "endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA", OMAMO provides the following ranking for potential model organisms:head -n 1 omamo_output_df.csv > ranked_organisms.csv
awk '$1 == 472'  omamo_output_df.csv >> ranked_organisms.csv
cat ranked_organisms.csv


GOnr	Species	QuerySpeciesGenes	ModelSpeciesGenes NrOrthologs	FuncSim_Mean	FuncSim_Std	Score
472	DICDI	NOP9;TBL3;ABT1	  Q551Y5;Q7KWS8;esf2	          3  	0.9095	0.1567	2.7286
472	NEUCR	NOP9;TBL3	         nop9;pod-5	          2  	1.0000	0.0000	2.0000
472	SCHPO	NOP9;TBL3	         nop9;utp13	          2  	1.0000	0.0000	2.0000OMAMO WebsiteYou can also visit theOMAMO website, where you can browse biological processes to study in 50 unicellular species.Change logVersion 0.2.1store ic values in hdf5 databaseVersion 0.2.0Overhaul and creating pip packageVersion 0.0.1Initial releaseCitationAlina Nicheperovich, Adrian M Altenhoff, Christophe Dessimoz, Sina Majidian, "OMAMO: orthology-based model organism selection", submitted to Bioinformatics journal,preprint.LicenseOMAMO is a free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.OMAMO is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.You should have received a copy of the GNU Lesser General Public License along with OMAMO. If not, seehttp://www.gnu.org/licenses/.