biocore / metagenomics_pooling_notebook / 7257554244
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Dev (#160)

* Spike in Analysis ported from R (#97)

* spike in analysis ported from R in two parts.  Can calculate coefficients for linear models to correct from relative to absolute abundance.  Can rescale relative abundance read counts to absolute abundance read counts, relative abundance cell counts, or absolute abundance cell counts.  TODO: absolute abundance cell counts per gram

* Updated file paths to be based from root of the checkout

* Lint nonsense for ancient 80 character terminals

* More linter nonsense

* PR review comments

* Update rescale_counts.py (#104)

Removed function to generate read count output; updated function for generating cell counts to generate cell counts per gram of input sample material

* Update rescale_counts.py (#105)

Added back function needed for testing to work

* Update test_rescale_counts.py (#106)

* Update calculate_coefficients.py (#107)

Update variable names

* Update metadata_samples_plasmid_sequences.txt (#109)

Added column for sample input weights and updated pool variable name

* fixes most bugs

* trigger CI

* Testing results and notes

* init changes

* Add tests dp (#152)

* add final tests for pooling nb

* move compress_plates_exp file

* move plate map files

* fix filepath of platemaps in compression test

* move the files back

* more path errors

* more path errors 2

* fix tests monday oct 23

* flake8 changes

* revert to original version of 2 functions; comment out 2 test cases

* try 2: remove changes to functions; remove test cases

* working notebook

* flake8 fixes

* flake8 fix

* new notebook for NPH stool input calculation values

* Create abs_quant_sample_info_calc.yml

config file for abs quant sample information calculations

* Port Mackenzie's NPH_calc_df_SLURRY.ipynb functionality into modules and unit-test (#155)

* port to modules of Mackenzie's NPH_calc_df_SLURRY.ipynb functionality

* port to... (continued)

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