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release 2.0#225

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evanroyrees merged 227 commits intomainKwanLab/Autometa:mainfrom release-2.0.0KwanLab/Autometa:release-2.0.0Copy head branch name to clipboardFeb 8, 2022

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Commits on Nov 19, 2019

• init autometa 2

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• added template classes from autometa class diagram discussion

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Commits on Jan 22, 2020

• autometa 1.0 refactored. New cli and beginnings of User API. markers cutoffs reformatted. configurations added to handle executable and database dependencies. k-mer counting (multiprocessing capabl…

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• updated markers links and link to test_metagenome.config

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Commits on Jan 23, 2020

• removed unneeded class diagram doc and edit test config to display required options. updates to database handling and added timeit to main function calls.

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• bugfix to get_kingdoms assigning self.taxonomy using self.assign_taxonomy() and changed logger for diamond to debug. utilities timeit now is INFO level logging. some 'f' string formatting for kmers…

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• updates to suppress parallel warnings when running prodigal. updated noparallel arg to parallel so does GNU parallel disabled by default. updated config sections to reflect parameter change

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• added coverage calculation handling for reads,sam,bam and bed files. Updated coverage.py args and metagenome.py and autometa.py to reflect new args. added respective files under [files] section in …

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• updated logger to DEBUG for majority_vote.py updated argparse help for --out in coverage.py and moved return statement in taxon assignment in metagenome.py to reduce redundancy.

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Commits on Jan 24, 2020

• updates to autometa configuration. Added kingdom arg to tune for only binning respective to selected kingdom. Choices are bacteria and archaea. bugfix where environs were being placed under databas…

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• suppressed parallel warnings when running hmmscan

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• bugfix to parallel warning supression for hmmscan

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Commits on Jan 27, 2020

• bugfix to orf calling in metagenome.py

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• upadted default config to handle coverage calculation files

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Commits on Jan 28, 2020

• update files in default.config

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Commits on Feb 2, 2020

• Add django-related files, clean up structure

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• Merge branch 'dev' of github.com:WiscEvan/Autometa into dev

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• Update ignore, force recache of un-ignored files

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• Update ignore, force recache of un-ignored files

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• Add vscode ignorance

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• Add vscode ignorance

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• Begin django website dev

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• Begin django website dev

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• Restart website, add first app

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• Restart website, add first app

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• Make startpage

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• Make startpage

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• Delete website; confusing naming

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• Delete website; confusing naming

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• Start new django website

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• Start new django website

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• Create startpage

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• Create startpage

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Commits on Feb 4, 2020

• bugfix to hmmer marker filtering (filepath handling). minor logging edits to lca and majority vote. removed unneccessary comment in metagenome. Comment in kmers to silence UMAP warnings.

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• Add startpage

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• Add startpage

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• Merge branch 'dev' of github.com:WiscEvan/Autometa into dev

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• Merge branch 'dev' of github.com:WiscEvan/Autometa into dev

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• Add template, css, bootstrap

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• Add template, css, bootstrap

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• Fix links, add nav-bar, css

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• Fix links, add nav-bar, css

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• Change blog template to autometa related terms

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• Change blog template to autometa related terms

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Commits on Feb 6, 2020

• Add Projects and Jobs as Models

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• Add Projects and Jobs as Models

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• Add login logout profile pages

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• Add login logout profile pages

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• Use conda env instead of pip

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• Use conda env instead of pip

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Commits on Feb 7, 2020

• Revert "Use conda env instead of pip"

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• Revert "Add login logout profile pages"

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• Revert "Change blog template to autometa related terms"

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• Revert "Fix links, add nav-bar, css"

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• Revert "Add template, css, bootstrap"

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• Revert "Merge branch 'dev' of github.com:WiscEvan/Autometa into dev"

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• Revert "Add startpage"

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• removed website dir and files (secrets published)

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• Revert "Use conda env instead of pip"

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• Revert "Add Projects and Jobs as Models"

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• Revert "Change blog template to autometa related terms"

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• Revert "Fix links, add nav-bar, css"

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• Revert "Add template, css, bootstrap"

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• Revert "Merge branch 'dev' of github.com:WiscEvan/Autometa into dev"

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• removed website dir and files (secrets published)

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Commits on Feb 10, 2020

• Merge branch 'dev' of https://github.com/KwanLab/Autometa into dev

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Commits on Feb 11, 2020

• updated directory structure, README.md, moved tests to their own directory with 78Mbp simulated community. updated config files. py2.7 bhsne for kmers in its own script to run py2.7 version. remove…

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Commits on Mar 3, 2020

• Added checkpointing functionality in utilities.py. updated config to reflect checkpointing. Renamed MAG class to Mag to follow python conventions. Added prodigal parsing to lca.py. Reflected in maj…

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• updated prodigal parsing into marker retrieval algorithm (markers.py and hmmer.py). By default will pass in ORFs retrieved from Mag object.

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Commits on Mar 5, 2020

• Merge pull request #8 from WiscEvan/dev

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• resolved #10 Contributors added and copyright year updated to 2020.

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• resolved #10 Contributors added and copyright year updated to 2020.

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• Merge branch 'master' of https://github.com/KwanLab/Autometa into dev

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Commits on Mar 11, 2020

• Resolves #16, Resolves #17 and simplified config parsing. Renamed 'projects' to 'workspace' to avoid confusion with 'project'. test metagenome.config file has been updated with respective files & p…

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• fixed merge conflicts

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Commits on Mar 12, 2020

• updates to project configuration handling metagenome numbering. Now retrieves versions from each executable dependency in environ.py. This is used in prodigal to parse corresponding to the prodigal…

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Commits on Mar 13, 2020

• significant simplification in API. Created Databases class in databases.py for handling databases config. Default behavior is to download and format required databases. Changed flag to flag to be m…

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Commits on Mar 15, 2020

• updates to check dependencies and control of debugging information when checking dependencies. Executable versions are now logged in debug info. log is now only written when flag is supplied. Times…

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• updated 'get_versions' function to return the version string if a program is provided as input. Updated respective files using this function. This should be clearer than returning a dict of the pro…

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• hotfix to case where new project does not contain any metagenomes. skip performing check to place appropriate metagenome number and just return 1.

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Commits on Mar 16, 2020

• Changed OSError to subclass ChildProcessError in prodigal.py. This is a bug fix related to exception hierarchy. changed timeit logging message format. Respective exception handling updatedin metage…

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Commits on Mar 17, 2020

• mostly resolves #21 and resolves #18.

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Commits on Mar 18, 2020

• resolved #19 added docstring, fixed nproc and removed depth function

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• Revert "resolved #19, did not add the copyright and liscence information"

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• resolved #19 added docstring (and liscence), fixed nproc and removed depth function

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• resolved #19 made the improvements as suggested by Evan

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• resolved #19 made the improvements_2 as suggested by Evan

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• resolved #19 made change bam.file to alignment.bam file

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Commits on Mar 19, 2020

• resolved #19 improved the cmd function

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• fix to extract contigs from orf_ids using specific prodigal version. Note: entire pipeline currently assumes orf calling was performed using prodigal. Update to template.py where ArgumentParser now…

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Commits on Mar 21, 2020

• resolved #19 removed run function, removed intermedediate files and renamed stderr and stdout

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Commits on Mar 23, 2020

• updated pandas numpy module call for nan to pd.NA from pandas version 1.0. in kmers and recursive_dbscan. Updated main function for recursive dbscan with required coverage table input and subsettin…

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Commits on Mar 24, 2020

• resolved #19 all intermediate files are now being deleted, added additional line in the end, and used o.path.dirname(os.path.abspath(otput.bam))

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• resolved #19 removed 'tail' from variable name, raise TypeError is nproc not int

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• update to docstrings added new file key in config and comma-delimited list handling for multiple reads files in input. Added fasta format check and simple fasta parser from Biopython for performanc…

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• returning from main rather than unnecessary sys import.

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Commits on Mar 25, 2020

• resolved #19 Temporary directory will now be delted under any circumstance

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Commits on Mar 26, 2020

• Merge pull request #25 from WiscEvan/dev

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• resolved #19 added FileNotFoundError, addressed other variable name issues

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• Merge branch 'dev' into dev

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• resolved #19 added docstring, fixed nproc and removed depth function

  

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• Revert "resolved #19, did not add the copyright and liscence information"

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• resolved #19 added docstring (and liscence), fixed nproc and removed depth function

  

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• resolved #19 made the improvements as suggested by Evan

  

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• resolved #19 made the improvements_2 as suggested by Evan

  

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• resolved #19 made change bam.file to alignment.bam file

  

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• resolved #19 improved the cmd function

  

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• resolved #19 removed run function, removed intermedediate files and renamed stderr and stdout

  

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• resolved #19 all intermediate files are now being deleted, added additional line in the end, and used o.path.dirname(os.path.abspath(otput.bam))

  

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• resolved #19 removed 'tail' from variable name, raise TypeError is nproc not int

  

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• resolved #19 Temporary directory will now be delted under any circumstance

  

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• resolved #19 added FileNotFoundError, addressed other variable name issues

  

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• Merge branch 'dev' of https://github.com/Sidduppal/Autometa into dev

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Commits on Apr 3, 2020

• Documentation (#34)

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Commits on Apr 12, 2020

• Issue #5 Working conda recipe (#38)

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Commits on Apr 15, 2020

• bug found in logger message within func where args was being passed. (#49)

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Commits on Apr 16, 2020

• fixes #2 (#47)

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Commits on Apr 21, 2020

• Contributing Guidelines (#50)

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Commits on May 5, 2020

• Add entrypoint functionality. Update docstrings.

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• Update MAG class to MetaBin.

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Commits on May 6, 2020

• 🎨📝💚 Add Markers class documentation. (#62)

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• 🎨📝 Rename --debug to --verbose flag (#63)

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• 🎨📝 Add functionality to bin without taxonomy. Update docstrings. (#65)

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• Add Documentation. Add readthedocs.org integration (#45)

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• Remove merge conflict resolution lines (Fixes #68) (#69)

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• Add mock import of modules and link to contribution guidelines (fixes #22) (#70)

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• Add docs badge

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• Update README.md

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Commits on May 13, 2020

• 🎨 🐎 Resolves #55 (#76)

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• Merge branch 'dev' of https://github.com/KwanLab/Autometa into issue-#54

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• 📝 Add docstrings to class properties.

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• Merge branch 'issue-#54' of https://github.com/WiscEvan/Autometa into issue-#53

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• 📝 Update describe property GC statement.

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Commits on May 14, 2020

• fixes-#54 Metagenome (#66)

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• Resolved merge conflicts with WiscEvan-issue-#53

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• Merge branch 'WiscEvan-issue-#53' into dev

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• hmmer (#72)

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