Study file optimization

[bedroesb]

• [x] Factor modality in investigation file - study file
• [x] Characteristics in study file
• [x] NCBI taxon Ids for Organism
• [x] non mandatory columns that are empty not showing
• [x] not making use of NA -> empty string
• [ ] get rid of Protocol REF column

[bedroesb]

Examples:

s_RIGW1.txt:

Source Name	Characteristics[Organism]	Characteristics[Genus]	Characteristics[Species]	Characteristics[Infraspecific Name]	Characteristics[Material Source ID]	Characteristics[Material Source DOI]	Protocol REF	Sample Name	Characteristics[Observation Unit Type]	Characteristics[Spatial Distribution]
Gewurztraminer Rs INRA-CV 925	NCBI:29760	Vitis	vinifera	subsp. vinifera cv. Gewurztraminer	258Col643	https://doi.org/10.15454/XAUWO4	sample collection	26730	BLOCK>PLOT	[X]29; [Y]22; [BLOCK>PLOT]26730; [BLOCK]2
Gewurztraminer Rs INRA-CV 925	NCBI:29760	Vitis	vinifera	subsp. vinifera cv. Gewurztraminer	258Col643	https://doi.org/10.15454/XAUWO4	sample collection	26511	BLOCK>PLOT	[X]22; [Y]4; [BLOCK>PLOT]26511; [BLOCK]1
Gewurztraminer Rs INRA-CV 925	NCBI:29760	Vitis	vinifera	subsp. vinifera cv. Gewurztraminer	258Col643	https://doi.org/10.15454/XAUWO4	sample collection	26310.22	BLOCK>PLOT>PLANT	[X]15; [Y]22; [plant]26310.22; [BLOCK>PLOT>PLANT]26310.22; [BLOCK>PLOT]26310; [BLOCK]2
Gewurztraminer Rs INRA-CV 925	NCBI:29760	Vitis	vinifera	subsp. vinifera cv. Gewurztraminer	258Col643	https://doi.org/10.15454/XAUWO4	sample collection	26310	BLOCK>PLOT	[X]15; [Y]22; [BLOCK>PLOT]26310; [BLOCK]2

s_BTH_Colmar_2000_SetB1.txt:

Source Name	Characteristics[Organism]	Characteristics[Genus]	Characteristics[Species]	Characteristics[Infraspecific Name]	Characteristics[Material Source ID]	Characteristics[Material Source DOI]	Protocol REF	Sample Name	Characteristics[Observation Unit Type]	Factor Value[itk]
ALBERIC	NCBI:4565	Triticum	aestivum	subsp. aestivum	13712	https://doi.org/10.15454/HZTT8F	sample collection	AlbericitktRep0	VIRTUAL_TRIAL	treated
APACHE	NCBI:4565	Triticum	aestivum	subsp. aestivum	13481	https://doi.org/10.15454/V8WRHY	sample collection	ApacheitktRep0	VIRTUAL_TRIAL	treated
CF00188	NCBI:4565	Triticum	aestivum	subsp. aestivum	CF00188	gnpis_pui:unknown:Wheat:CF00188	sample collection	CF00188itktRep0	VIRTUAL_TRIAL	treated
CF00189	NCBI:4565	Triticum	aestivum	subsp. aestivum	20362	https://doi.org/10.15454/RWJVRH	sample collection	CF00189itktRep0	VIRTUAL_TRIAL	treated

s_VIB_study___40.txt:

Source Name	Characteristics[Organism]	Characteristics[Genus]	Characteristics[Species]	Protocol REF	Sample Name	Characteristics[Observation Unit Type]	Characteristics[Spatial Distribution]
B73 RIL 8-way	NCBI:4577	Zea	mays	sample collection	pot_180	plant	[plant]180
B73 RIL 8-way	NCBI:4577	Zea	mays	sample collection	pot_173	plant	[plant]173
B73 RIL 8-way	NCBI:4577	Zea	mays	sample collection	pot_178	plant	[plant]178
B73 RIL 8-way	NCBI:4577	Zea	mays	sample collection	pot_172	plant	[plant]172

[bedroesb]

@cpommier

[bedroesb]

This turns out to be a stable solution for the study file generation