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hitsFromSuppOrth reads suppOrth.tsv into a blastStructure for getModelFromHomology, in both directions, with filters on support, predictors, identity and e-value, and mapping of protein ids to gene ids. runSuppOrth runs the suppOrth command and reads its output. Matches hits_from_supporth and run_supporth in raven-toolbox.
Function test results399 tests 360 ✅ 1m 32s ⏱️ Results for commit fb7df09. |
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Development of this pull request continues in CompMetEng/RAVEN#4, which has the same commits on the copied history. |
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Main improvements in this PR:
hitsFromSuppOrthreads the consensus orthologs of SuppOrth (suppOrth.tsv) into ablastStructureforgetModelFromHomology. Each pair between the new organism and a template is written in both directions. Pairs can be filtered on the number of supporting predictors (minSupport), on required predictors (requireTools), and on SuppOrth's identity and e-value.proteinToGenemaps protein ids to gene ids (cell array,containers.Map, JSON or tab-separated file), taking the highest support over isoform pairs.speciesToModelrenames species or leaves them out. The e-value, identity, alignment length and ppos are placeholders that pass the filters ofgetModelFromHomology; the bitscore is SuppOrth's own, which strictness 3 ranks by. SuppOrth's values per gene pair are returned as a second output.runSuppOrthruns thesuppOrthcommand (from thesuppOrthargument, theRAVEN_SUPPORTHenvironment variable, or the PATH) on the proteomes of the new organism and the templates, with the model ids as species labels, and reads the result withhitsFromSuppOrth. Proteomes that share protein ids are passed with a per-species prefix that is removed from the hits. SuppOrth's output is written torun_supporth.log, and a failed run raises an error with the end of that output. SuppOrth's predictors do not run on Windows, whererunSuppOrthraises an error.getModelFromHomology,getBlast,getDiamondandmakeFakeBlastStructurerefer to the new functions.tReconstructionhas tests for reading, filtering, species and gene mapping, the path throughgetModelFromHomologyat strictness 1–3, andrunSuppOrthagainst a stub command.The functions match
hits_from_supporthandrun_supporthin raven-toolbox (SysBioChalmers/raven-toolbox#171). On a SuppOrth run with OrthoFinder, SonicParanoid and Broccoli of Kluyveromyces lactis (UniProt UP000000598) against Saccharomyces cerevisiae (SGDorf_trans), with yeast-GEM 9.1.1 as template, both give the same hits and the same draft models (reactions and grRules) forminSupport1–3 and strictness 1–3.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.