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* added fDOG-Assembly workflow * added fDOG-Assembly dependencies * adjustments to new muscle version and fDOG version * further changes to adapt to new fDOG version * script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file * deactivate fas config output * Bugfix muscle v5 command in fdog.addCoreGroup * fixed augustus version * further updates to adapt fDOG-Assembly to the new fDOG version. Additionally bugfix in co-ortholog detection if MSA crashed due to too many sequences. * contig fasta files where delited from the tmp folder to save memory * add function to output only best isoform * added function to only output one isoform * new gff function, fixed problem that muscle can not work with path containing @ sysmbols, adapted mergeOutput that merges files with _og ending * Fixed bug where fDOG-Assembly does not terminate if FAS raises an error * bugfix createGff function * bugfix createGff function --------- Co-authored-by: trvinh <trvinh@gmail.com>
fDOG-Assembly bug fix during distance calculation: AS U will be scored as C
Update fDOG version Bug fix addAssembly user output --------- Co-authored-by: trvinh <trvinh@gmail.com>
* bug fix debug mode * updated check_ref_spec function * updated check_ref_spec function, added region output if augustus is used * update get_distance_function * bug fix check_ref_spec function * v 0.1.5.1 * update output containing candidate regions * bugfix --------- Co-authored-by: trvinh <trvinh@gmail.com>
* Updated fdog.addAssembly module * improved call of main fuction * Improved help function
…_assembly" This reverts commit 7b656af.
This reverts commit 5414d1b.
This reverts commit 5b458ea.
* removed bio.applications * version bump * update python version in github build * Update github_build.yml (#50) * replaced pkg_resources by importlib.metadata * replaced pkg_resources by importlib.metadata * Update README.md * replaced bio.applications in checkData * added option to use micromamba and mamba install * add option to use micromamba, mamba or conda * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * version bump * Update README.md * Update README.md (#53) * Update README.md * Update README.md (#54) * Update README.md --------- Co-authored-by: trvinh <trvinh@gmail.com>
* removed bio.applications * version bump * update python version in github build * Update github_build.yml (#50) * replaced pkg_resources by importlib.metadata * replaced pkg_resources by importlib.metadata * Update README.md * replaced bio.applications in checkData * added option to use micromamba and mamba install * add option to use micromamba, mamba or conda * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * version bump * Update README.md * Update README.md (#53) * Update README.md * Update README.md (#54) * Update README.md --------- Co-authored-by: trvinh <trvinh@gmail.com>
* added fDOG-Assembly workflow * added fDOG-Assembly dependencies * adjustments to new muscle version and fDOG version * further changes to adapt to new fDOG version * script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file * script to produce msa and hmm in the format fDOG-Assembly requires from a fasta file * Bugfix muscle v5 command in fdog.addCoreGroup * fixed augustus version * further updates to adapt fDOG-Assembly to the new fDOG version. Additionally bugfix in co-ortholog detection if MSA crashed due to too many sequences. * contig fasta files where delited from the tmp folder to save memory * Revert "Merge branch 'fdog-assembly' of https://github.com/mueli94/fDOG-Assembly into fdog-assembly" This reverts commit d688bbb, reversing changes made to 5068b7a. * bugfix for installation with miniconda and removal of MetaEuk tmp folder * Update .gitignore * add function to output only best isoform * added function to only output one isoform * new gff function, fixed problem that muscle can not work with path containing @ sysmbols, adapted mergeOutput that merges files with _og ending * Fixed bug where fDOG-Assembly does not terminate if FAS raises an error * bugfix createGff function * bugfix createGff function * bugfix gff output * remove MetaEuk tmp files * bug fix during distance calculation: AS U (selenocystein) will be scored as C (cystein) * bug fix user output * bug fix debug mode * updated check_ref_spec function * updated check_ref_spec function, added region output if augustus is used * update get_distance_function * bug fix check_ref_spec function * v 0.1.5.1 * update output containing candidate regions * bugfix * Updated fdog.addAssembly module * improved call of main fuction * Improved help function * bugfix using --strict * bug fix consensus sequence will now use precomputed consensus sequences when offered also with MetaEuk * day end -> working on merging overlapping candidate regions * removed bio.applications * version bump * update python version in github build * Update github_build.yml (#50) * replaced pkg_resources by importlib.metadata * replaced pkg_resources by importlib.metadata * Update README.md * replaced bio.applications in checkData * added option to use micromamba and mamba install * add option to use micromamba, mamba or conda * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * replace ete3 by ete4 * version bump * Update README.md * Update README.md (#53) * Update README.md * Update README.md (#54) * Update README.md * update * fDOG merge * CheckCoorthologsRef is on per default * region merge start, experimental * bug fix checkCoorthologsRefOff * --checkCoorthologs parameter is enabled per default, has to be turned off by using --checkCoorthologsOff --------- Co-authored-by: Hannah <47216555+mueli94@users.noreply.github.com> Co-authored-by: trvinh <trvinh@gmail.com>
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Merge fdog-assembly to fdog