Environment and directory structure updates #8
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This is a temporary setup and could change later. For now, each user (class User read here: https://docs.djangoproject.com/en/3.0/ref/contrib/auth/) has projects (class Project) and each project has jobs (class Job). Each class creates a data table and is mapped to the related table using foreign keys. Please read more here: https://docs.djangoproject.com/en/3.0/ref/models/fields/#foreignkey
This reverts commit cbb42d4.
This reverts commit 4ec643d.
This reverts commit cc2d595.
This reverts commit 4d7c87b.
This reverts commit 0270bf1.
This reverts commit c2c5202.
This reverts commit aa1dbc1.
…ctory with 78Mbp simulated community. updated config files. py2.7 bhsne for kmers in its own script to run py2.7 version. removed shebang specifically specifying python3 to avoid cryptic errors where user defined python env is not selected when run. Added .gitignore to ncbi dir under databases to keep empty directory. Post-processing are in their own directory under validation.
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I'm going to have to finish my review of the refactored code first before I can assess this. Is that OK? I just would feel better understanding the code first. |
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Yes, no problem. Since I have a fork of the repository, I can operate on my own repo until the changes are merged. |
…reflect checkpointing. Renamed MAG class to Mag to follow python conventions. Added prodigal parsing to lca.py. Reflected in majority_vote.py. removed superfluous attributes for DiamondResult object. Updated metagenome.config with checkpoints.tsv file.
…and hmmer.py). By default will pass in ORFs retrieved from Mag object.
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This is partially to display the git workflow via forks, pull requests, reviews and merges. You do not need to do a comprehensive review here. These edits are minor and should work out some of the kinks I have encountered while testing on the Boreal datasets as well as on my Mac
Updates
tests/metagenome.configlca.pyto display thousand delimiter for ORFs search description.bhsne.pyunder binning directory to provide user capability to run python2.7 BH-tSNE (Note: conda env setup is withinbhsne.pyscript.hmmer.pymain script where input and output args were the same. Updated argparse parameters accordingly.kmers.pykmers.pyargs with default--n-components=2and--do-pcaas well as--pca-dimensionsare now available in the main call to kmers.Example usage of scripts populating datasets directory