Finish statistical eval#48

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finish_statistical_eval

Commits on May 18, 2021

Commits on May 31, 2021

add functions to calculate cazy fam freq across test sets
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add imports for calc cazy fam freq
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remove unused import
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add storing path to binary classification df to class instance
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update repr of class
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improve syntax formating
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update logger message to print path where looked for fasta files
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write out bootstrap results to output dir
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write output to out dir not the pwd
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write output to out dir not the pwd
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write output to out dir not the pwd
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add detail to cmd parser help message
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Merge branch 'finish_statistical_eval' of https://github.com/HobnobMancer/pyrewton into finish_statistical_eval
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add func that identified FP and FN binary predictions
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add function to retrieving the blast score ratio between a cazyme and non-cazyme
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update class instance attrbiute name
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correct getting tool total from the row
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add in determining which column to check depending if FP or FN
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add in call to function to identify binary FP and FN
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Commits on Oct 27, 2021

move all file-io related funcs to the file_io module

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create sep module for calling to Entrez

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create module for handling the parsing of genomes

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add more robust method for ensuring not introduction of duplicates

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move all genome retrieving and parsing funcs to a single submodule

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move funcs for downloading and parsing genomes to separate scripts

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update import paths

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move funcs for retrieving file/dir paths to file_io module

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remove duplicate func and update imports

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remove redundant script

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add TOC to README for evaluation of CPTs

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add copyright and liscence to scripts

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update installation instructions

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add func for getting genomes in dir

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add option to skip downloading genomes and parse previously downloaded genomes when creating test sets for eval

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add missing if __name__ = 'main'

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add --genomes flag to parser

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update import paths

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add retrieving packages to setup

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add params missing from funcs calls

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add handling when qualifier is not retrieved

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make warning message more verbose

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add option to extract seq to a subdir

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write test sets to user defined output dir

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add missing param from func call

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write out alignment scores to a sep dir

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add logging the CAZome coverage of the genome and sample size coverage of the CAZome
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add genomic accession to CAZome coverage file
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Commits on Nov 4, 2021

add missing requirements files and update requirements

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move common funcs to own submodule and import

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update import paths

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Commits on Nov 5, 2021

create single script for both 'create_test_sets_*.py' scrupts

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create separate scripts when using json or db to identify CAZy cataltouged CAZymes

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create separate scripts when using json or db to identify CAZy cataltouged CAZymes

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add ability to get CAZy annotations from dict or db

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add logging of genome and cazome coverage

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fix merge conflict issues

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parse to the stats module the source type for cazy annotations

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add missing cazy_webscraper sqlORM imports

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add missing cazy_webscraper sqlORM imports

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add calc fam freqs in the tests sets from the db

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remove unused scripts

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import genome get and parse funcs from saintBioutils

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add indpendent eval create test sets to the docs

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correct typo

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remove duplciate log
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update import paths
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remove func now imported from saintUtils
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remove funcs now imported from saintUtils
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import makeOutputDir from saintBioutils
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write out tab delimited list of test sets compositions
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correct type, so opens Path not list
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Update imports
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make output dir necessary when invoking cazyme classifeirs
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remove unneeded stdout check
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correct typo in docs
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remove unused variable
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update path check when invoking CAZyme classifers
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update path check when invoking CAZyme classifers
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update path for install cazyme classifiers
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update installation instructions
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update requirements
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add changing dir to ensure files are installed into the correct dir
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Commits on Nov 7, 2021

Commits on Nov 8, 2021

Commits on Nov 9, 2021

Commits on Nov 10, 2021

correct typo in file name
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Commits on Nov 11, 2021

update imports and improve colour gradient
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Commits on Nov 30, 2021

correct typo in txid
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correct typo in txid
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update imports

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update imports

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update imports

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add comparing taxa group binary classification comparison

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add tax groups to families prediction df

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return dfs not write to disk

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remove unused param from func call

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evaluate cazy fam performance per tax group

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move func for evaluating cazy fam perforamnce to fam eval script

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move func for evaluating cazy fam perforamnce to fam eval script

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add evaluate performance per cazy class per tax group

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remove funcs that are now imported

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add parsing input tax_groups YAML file

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add yaml config file for defining tax groups
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Merge branch 'finish_statistical_eval' of https://github.com/HobnobMancer/pyrewton into finish_statistical_eval
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add tax groups example file

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add tax groups example file

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update column names
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Merge branch 'finish_statistical_eval' of https://github.com/HobnobMancer/pyrewton into finish_statistical_eval
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Commits on Dec 1, 2021

write all class all test sets df with a separate column per stat param
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Commits on Dec 3, 2021

add identifying difficult cazy families
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Commits on Dec 4, 2021

add calc fam populations freq in test sets
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Commits on Jan 10, 2022

ignore fam annotation when retrieving consensus class annotation

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Commits on Jan 11, 2022

add parsing the file of recombining tools

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parse binary df, get consensus result for recombined tools

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pyrewton/cazymes/evaluate_tools/stats/binary_cazyme_noncazyme_classification.py

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make binary eval funcs more adapatable

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add calc binary stats for recombined tools

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add getting recombined tools consensus cazy class classification

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add calls to calc recombined tools cazy class classifications

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rename args short hand

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add missing params to func calls

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makes tools param to have default value

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write out parsed dfs

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specify the name of the tools to include in the analysis

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add recombined tool ground truths to the gt df

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get recombined tools cazy family consensus predictions

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remove duplicate use of short hand -b

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move calling var to after it is defined

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Commits on Jan 17, 2022

add new created rows to list of all rows

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add new created rows to list of all rows

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remove unused column names when adding data to the GT df

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add comments to improve readability

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update docstrings

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