Scripts to find and manipulate orthologous
Check the list of ortologous pairs from OMA and separate the uniq orthologous transcripts ID. Used (in my case) to get a list of uniq transcripts from each pair of species to get the final orthologous among all tested species.
Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Usage List_uniqOrtho.py -i pair file -1 sp1 outprefix -2 sp2 outprefix
Where -i = orthologous pair file result from OMA for any two species -1 = prefix of the outuput list for sp1 in the OMA file -2 = prefix of the outuput list for sp2 in the OMA file
Options -h for usage help
Compare the list of orthologous from one species in different lists. Ex. genes of sp1 orthologous to sp2 and sp3. Used (in my case) to get a list of orthologous among the different species (from pair othologou analyses in OMA).
Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Usage Shared_Ortho.py -1 ortho_sp2 -2 ortho_sp3 -o output
Where -1 = list of orthologous genes between the species of interest and sp2 -2 = list of orthologous genes between the species of interest and sp3 -o = name of the output file. List of genes from the species of interest orthologous to the other species
Options -h for usage help
Check the list of ortologous pairs from OMA and separate the orthologous of interest based on a list of ID provided by the user. Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Developed (in my case) to get only the orthology data from the genes that appear in all species.
Usage Select_Ortho.py -i pair file -l list_interest -o output
Where pair file = orthologous pair file result from OMA for any two species list_interest = list of the genes ID you want to recover from the pair file (one per line). Only get the sp1 ID. output = output with the orthology info (like reported by OMA) of the genes from the interest list
Options -h for usage help
Check the list of ortologous pairs from OMA and separate the orthologous of interest based on a list of ID provided by the user. Like Selcte_Ortho.py but for other input format Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Developed (in my case) to get only the orthology data from the genes that appear in all species (file format after cleaning 1-1).
Usage Select_Ortho2.py -i pair file -l list_interest -o output
Where pair file = orthologous pair file result from OMA for any two species list_interest = list of the genes ID you want to recover from the pair file (one per line). Only get the sp1 ID. output = output with the orthology info (like reported by OMA) of the genes from the interest list
Options -h for usage help
Select only one orthologous from a 1:multi orthologous data (reported by OMA pairwise analyses).
Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Usage One_Multi.py -i 1:multi -o output prefix
Where -i = table as the output from pairwise orthology analyses in OMA but only with 1:multi orthologous type -o = prefix for the output files. 2 outputs will be generated: 1- prefix_OMA.txt, table containing the orthologous pairs determinied by OMA as one group; 2- prefix_nogroup.txt, table containing the putative orthologous pairs to be chosen by the user.
Options -h for usage help
Select only one orthologous from a multi:1 orthologous data (reported by OMA pairwise analyses).
Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Usage Multi_One.py -i multi:1 -o output prefix
Where -i = table as the output from pairwise orthology analyses in OMA but only with multi:1 orthologous type -o = prefix for the output files. 2 outputs will be generated: 1- prefix_OMA.txt, table containing the orthologous pairs determinied by OMA as one group; 2- prefix_nogroup.txt, table containing the putative orthologous pairs to be chosen by the user.
Options -h for usage help
Select only one orthologous from a multi:multi orthologous data (reported by OMA pairwise analyses).
Ref.: Altenhoff A et al., The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Research, 2015, 43 (D1): D240-D249 (doi:10.1093/nar/gku1158).
Usage Multi_Multi.py -i multi:multi -o output prefix
Where -i = table as the output from pairwise orthology analyses in OMA but only with multi:multi orthologous type -o = prefix for the output files. 2 outputs will be generated: 1- prefix_OMA.txt, table containing the orthologous pairs determinied by OMA as one group; 2- prefix_nogroup.txt, table containing the putative orthologous pairs to be chosen by the user.
Options -h for usage help