epimuller 0.0.5

Visualize lineages overtime, with phylogentic context, based on viral genomes

epiMuller README

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

Documentation avaliblity

Read the Docs

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

Visulize default aa mutation list

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

Visulize a trait: lineage

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 \

Visulize your own aa mutation list

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 gitHub

	- 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 epimuller-draw/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 in epimuller folder 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 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.