Parsing prediction tool output#45

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HobnobMancer wants to merge 122 commits intomasterfrom

parsing_prediction_tool_output

Commits on Nov 3, 2020

start to write out shell script for install pyrewton and all requirements including third part tools
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Commits on Nov 10, 2020

factorise building prediction queries and invoking tools to a separate function from main()
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remove white space
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add dict instance to data class to store output file paths as they are created
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add creation, retrieval and adding of path to the tools output files to each Query class instance
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build dictionary containing path to tools output files
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add tqdm progress bars
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add tqdm progress bars
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fix typo and line length issues
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factorise out coordinating the standardising the prediction tools outputs to a function separate from main()
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Commits on Nov 13, 2020

Commits on Nov 17, 2020

Commits on Nov 23, 2020

Commits on Nov 24, 2020

Commits on Nov 25, 2020

add notebook for planning parsing of prediction tools output

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add functions to parse tool output from 'parsing_prediction_tool_output' jupyter notebook

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Delete finding_a_consensus_result.ipynb

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remove print statements, reorder functions

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factorise building prediction queries and invoking tools to a separate function from main()

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remove white space

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add dict instance to data class to store output file paths as they are created

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add creation, retrieval and adding of path to the tools output files to each Query class instance

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build dictionary containing path to tools output files

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add tqdm progress bars

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add tqdm progress bars

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fix typo and line length issues

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factorise out coordinating the standardising the prediction tools outputs to a function separate from main()

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reorder functions so follows order of data processing and move call to get_fasta_paths out of main()

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make single call to function that will coordinate standarising output, statistical evaluationa and writing summary reports from main() and then program closes

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update variable names so they are consistent and clearer as to what they relate

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factorise out preparing args for and invoking prediction tools, so invoking each prediction tool is invoked by its own function

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updae retrieval of output from invoke_prediction_tools()

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move coordiantion of standardising output and retrieving paths to output files to separate functions

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update parameters in functin call

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add writing out of dataframes to disk

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add quality checking to parsing of cupp output

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import, correct syntax error of logger, and remove white space

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add missing params to function call and remove whitespace, and add spaces after separators in function calls

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add quality checking for parsing ecami

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shorten long lines and remove white space

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shorten long line

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add logging and checking if cannot find ecami or cupp output file

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move all dbCAN parsing functions to a separate script

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move functions for parsing CUPP output to a separate script

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move functions for parsing eCAMI output to a separate script

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remove redundant functions copies from file as these have been moved to separate scripts

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add logging if EC number is in non-standard format when parsing CUPP

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add quality checking for retrieving ec numbers and cazy (sub)families, add logging of irregularities

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add missing ')' and remove white space

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remove comments adding reminders to add logging

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add detail of consequences of catching error to logger messages

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add details of consequences of error catching and add error catching if can't open output files

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update function calls for parsing prediction tool outputs

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add check if dataframe is None to raise error and pass

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Delete process_cazyme_predictions.py

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Delete cazyme_class_evaluation.py

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Delete binary_cazyme_evaluation.py

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Delete __init__.py

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removed uneeded empty dicyionary
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correct moving up dir from ../ to ..
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update capturing taxid to not be NCBI specific
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add function call () to end of iterdir
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fix catching and logging when no output files are found
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remove print statements
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correct changing dir using ../ to ..
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correct name of CUPP prediction python file
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Commits on Nov 26, 2020

add print statemetns to track progress
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save local changes, fixing merge conflict
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Commits on Nov 27, 2020

write CTP output to terminal and log file
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