Metadata-Version: 2.1
Name: epimuller
Version: 0.0.4
Summary: Visualize lineages overtime, with phylogentic context, based on viral genomes
Home-page: https://github.com/jennifer-bio/epimuller
Author: Jennifer L Havens
Author-email: jhavens@ucsd.edu
License: MIT license
Description: # epiMuller README
        
        ![Muller plot image](https://raw.githubusercontent.com/jennifer-bio/epiMuller/main/images/case_scaled_lineages_long.png)
        
        ##### About
        
        ###### Author
        Jennifer L Havens
        
        ###### Purpose
        Visualize lineages overtime, with phylogentic context, based on viral genomes
        
        ###### Language
        Python3
        
        ###### Inputs
        Alingment, collection date, PANGO lineage, Nextstain JSON files, and timetree
        
        ###### Source code avaliblity
        [gitHub](https://github.com/jennifer-bio/epimuller)
        
        ###### Documentation avaliblity 
        [Read the Docs](https://epimuller.readthedocs.io/en/stable/)
        
        ## Quick start
        
        ```
        pip install epimuller
        
        epimuller [-h] [-oDir OUTDIRECTORY] -oP OUTPREFIX -n
        	 INNEXTSTRAIN -m INMETA [-p INPANGOLIN]
        	 [-f TRAITOFINTERSTFILE]
        	 [-k TRAITOFINTERSTKEY]
        	 [-aa AAVOCLIST [AAVOCLIST ...]]
        	 [-t TIMEWINDOW] [-s STARTDATE] [-e ENDDATE]
        	 [-mt MINTIME] [-min MINTOTALCOUNT]
        	 [-c CASES_NAME] [-l {date,time}]
        	 [-lp {Right,Max,Start,End}]
        
        ```
        
        ## SOME EXAMPLES 
        
        #### Examples for full run 
        To prep files for these examples for epimuller look at Example_CommandsFromScratch.txt
        ```
        epimuller \
        	-n inputData/GISAID_NYCPHL_04_29/02_nextstrainResults \
        	-m inputData/GISAID_NYCPHL_04_29/gisaid_2021_04_30_00_rename.tsv \
        	-oDir 03_results_NYCPHL_April29 \
        	-oP 01_defaultAAList \
        	-c inputData/CITY_US-NY_NYC_outbreakinfo_epidemiology_data_2021-04-30.tsv
        
        epimuller \
        	-n inputData/GISAID_NYCPHL_04_29/02_nextstrainResults \
        	-m inputData/GISAID_NYCPHL_04_29/gisaid_2021_04_30_00_rename.tsv \
        	-oDir 03_results_NYCPHL_April29 \
        	-oP 02_pangolin \
        	-c inputData/CITY_US-NY_NYC_outbreakinfo_epidemiology_data_2021-04-30.tsv \
        	--traitOfInterstFile traits.json \
        	--traitOfInterstKey lineage \
        	-lp Max \
        	-min 100 \
        
        epimuller \
        	-n inputData/GISAID_NYCPHL_04_29/02_nextstrainResults \
        	-m inputData/GISAID_NYCPHL_04_29/gisaid_2021_04_30_00_rename.tsv \
        	-oDir 03_results_NYCPHL_April29 \
        	-oP 03_selectedAA \
        	-c inputData/CITY_US-NY_NYC_outbreakinfo_epidemiology_data_2021-04-30.tsv \
        	-aa 'SE484K' 'S*452*' \
        	-min 50 \ 
        	-mt 20
        ```
        
        
        ## Known edge cases / featrues to add  
        Known edge cases which are not correctly dealt with or features I intend to add (that I will get around to fixing eventually) 
        If you run into anything else please let me know on https://github.com/jennifer-bio/epimuller
        ```
        	- nt_muts ; not set up for nt mutations (only amino acid or trait)
        	- only takes nextstrain json files - intending to set up to take treetime output
        	- feel free to ignore the undefined.svg that gets made - it is related to checking the size of the text to space out labels
        	- add plot and font size to arg options
        ```
        
        ## Addtional features
        
        ##### Color
        If you would like to specify color for clade: in --parentHierarchy_name file (of drawMuller.py input) add col with name: "color" and hex color value (starting with #) for clades you want to specify.
        
        ##### Plot and font size
        In the file: scripts/drawMuller.py ; near top of script change value for desired WIDTH, HEIGHT , LEGENDWIDTH (space on right side of plot for labels), MARGIN, or FONTSIZE variables
        Then run with source code by > python scripts/drawMuller.py [Arugments]
        
        ##### Parse GISAID fasta for metadata
        epimuller-parse
        If you have downloaded sequences from GISAID under the search tab, you can parse out the names into a metadata file (format tested as of 2021-04-30)
        
        
        ## ARGUMENTS  
        
        ```
        optional arguments:
        	-h, --help            show this help message and exit
        
        Options for full repot:
        	-oDir OUTDIRECTORY, --outDirectory OUTDIRECTORY
        		folder for output (default: ./)
        	-oP OUTPREFIX, --outPrefix OUTPREFIX
        		prefix of out files withen outDirectory (default:
        		None)
        
        Options passed to epimuller-define:
        	-n INNEXTSTRAIN, --inNextstrain INNEXTSTRAIN
        		nextstrain results with tree.nwk and
        		[traitOfInterst].json (default: None)
        	-m INMETA, --inMeta INMETA
        		metadata tsv with 'strain' and 'date'cols, optional:
        		cols of trait of interst; and pangolin col named:
        		'lineage' or 'pangolin_lin' (default: None)
        	-p INPANGOLIN, --inPangolin INPANGOLIN
        		pangolin output lineage_report.csv file, if argument
        		not supplied looks in inMeta for col with
        		'pangolin_lin' or 'lineage' (default: metadata)
        	-f TRAITOFINTERSTFILE, --traitOfInterstFile TRAITOFINTERSTFILE
        		name of nextstrain [traitOfInterst].json in
        		'inNextstrain' folder (default: aa_muts.json)
        	-k TRAITOFINTERSTKEY, --traitOfInterstKey TRAITOFINTERSTKEY
        		key for trait of interst in json file (default:
        		aa_muts)
        	-aa AAVOCLIST [AAVOCLIST ...], --aaVOClist AAVOCLIST [AAVOCLIST ...]
        		list of aa of interest in form
        		[GENE][*ORAncAA][site][*ORtoAA] ex. S*501*, gaps
        		represed by X (default: None)
        	-t TIMEWINDOW, --timeWindow TIMEWINDOW
        		number of days for sampling window (default: 7)
        	-s STARTDATE, --startDate STARTDATE
        		start date in iso format YYYY-MM-DD or 'firstDate'
        		which sets start date to first date in metadata
        		(default: 2020-03-01)
        	-e ENDDATE, --endDate ENDDATE
        		end date in iso format YYYY-MM-DD or 'lastDate' which
        		sets end date as last date in metadata (default:
        		lastDate)
        
        Options passed to epimuller-draw:
        	-mt MINTIME, --MINTIME MINTIME
        		minimum time point to start plotting (default: 30)
        	-min MINTOTALCOUNT, --MINTOTALCOUNT MINTOTALCOUNT
        		minimum total count for group to be included (default:
        		10)
        	-c CASES_NAME, --cases_name CASES_NAME
        		file with cases - formated with 'date' in ISO format
        		and 'confirmed_rolling' cases, in tsv format (default:
        		None)
        	-l {date,time}, --xlabel {date,time}
        		Format of x axis label: ISO date format or timepoints
        		from start (default: date)
        	-lp {Right,Max,Start,End}, --labelPosition {Right,Max,Start,End}
        		choose position of clade labels (default: Right)
        
        ```
        
        
        
        ## Only make abundance and hiearchy files 
        
        ```
        usage: epimuller-define [-h] -n INNEXTSTRAIN -m INMETA [-p INPANGOLIN]
        	 [-f TRAITOFINTERSTFILE] [-k TRAITOFINTERSTKEY]
        	 [-aa AAVOCLIST [AAVOCLIST ...]]
        	 [-oDir OUTDIRECTORY] -oP OUTPREFIX
        	 [-t TIMEWINDOW] [-s STARTDATE] [-e ENDDATE]
        
        optional arguments:
        	-h, --help            show this help message and exit
        	-n INNEXTSTRAIN, --inNextstrain INNEXTSTRAIN
        		nextstrain results with tree.nwk and
        		[traitOfInterst].json (default: None)
        	-m INMETA, --inMeta INMETA
        		metadata tsv with 'strain' and 'date'cols, optional:
        		cols of trait of interst; and pangolin col named:
        		'lineage' or 'pangolin_lin' (default: None)
        	-p INPANGOLIN, --inPangolin INPANGOLIN
        		pangolin output lineage_report.csv file, if argument
        		not supplied looks in inMeta for col with
        		'pangolin_lin' or 'lineage' (default: metadata)
        	-f TRAITOFINTERSTFILE, --traitOfInterstFile TRAITOFINTERSTFILE
        		name of nextstrain [traitOfInterst].json in
        		'inNextstrain' folder (default: aa_muts.json)
        	-k TRAITOFINTERSTKEY, --traitOfInterstKey TRAITOFINTERSTKEY
        		key for trait of interst in json file (default:
        		aa_muts)
        	-aa AAVOCLIST [AAVOCLIST ...], --aaVOClist AAVOCLIST [AAVOCLIST ...]
        		list of aa of interest in form
        		[GENE][*ORAncAA][site][*ORtoAA] ex. S*501*, gaps
        		represed by X (default: None)
        	-oDir OUTDIRECTORY, --outDirectory OUTDIRECTORY
        		folder for output (default: ./)
        	-oP OUTPREFIX, --outPrefix OUTPREFIX
        		prefix of out files withen outDirectory (default:
        		None)
        	-t TIMEWINDOW, --timeWindow TIMEWINDOW
        		number of days for sampling window (default: 7)
        	-s STARTDATE, --startDate STARTDATE
        		start date in iso format YYYY-MM-DD or 'firstDate'
        		which is in metadata (default: 2020-03-01)
        	-e ENDDATE, --endDate ENDDATE
        		end date in iso format YYYY-MM-DD or 'lastDate' which
        		is in metadata (default: lastDate)
        ```
        
        
        ## Only plot 
        
        ```
        usage: epimuller-draw [-h] -p PARENTHIERARCHY_NAME -a ABUNDANCE_NAME
        	 [-c CASES_NAME] -o OUTFOLDER [-mt MINTIME]
        	 [-min MINTOTALCOUNT] [-l {date,time}]
        	 [-lp {Right,Max,Start,End}]
        
        optional arguments:
        	-h, --help            show this help message and exit
        	-p PARENTHIERARCHY_NAME, --parentHierarchy_name PARENTHIERARCHY_NAME
        		csv output from mutationLinages_report.py with child
        		parent col (default: None)
        	-a ABUNDANCE_NAME, --abundance_name ABUNDANCE_NAME
        		csv output from mutationLinages_report.py with
        		abundances of clades (default: None)
        	-c CASES_NAME, --cases_name CASES_NAME
        		file with cases - formated with 'date' in ISO format
        		and 'confirmed_rolling' cases, in tsv format (default:
        		None)
        	-o OUTFOLDER, --outFolder OUTFOLDER
        		csv output from mutationLinages_report.py with child
        		parent col (default: None)
        	-mt MINTIME, --MINTIME MINTIME
        		minimum time point to start plotting (default: 30)
        	-min MINTOTALCOUNT, --MINTOTALCOUNT MINTOTALCOUNT
        		minimum total count for group to be included (default:
        		10)
        	-l {date,time}, --xlabel {date,time}
        		Format of x axis label: ISO date format or timepoints
        		from start (default: date)
        	-lp {Right,Max,Start,End}, --labelPosition {Right,Max,Start,End}
        		choose position of clade labels (default: Right)
        
        ```
        
        ## Citation
        
        Please [link to this github](https://github.com/jennifer-bio/epimuller) if you have used epimuller in your research. 
        
        #### Extra notes on GISAID
        
        If you do use GISAID data please acknowledge the contributers, such as with [language suggested by GISAID](https://www.gisaid.org/help/publish-with-data-from-gisaid/).
        
Keywords: epimuller
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.7
Description-Content-Type: text/markdown
