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genophenoenvo / terraref-datasets

Repository for code and small datasets derived from the TERRA REF program
MIT License
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prototype tall to wide script #57

Closed kshefchek closed 4 years ago

kshefchek commented 4 years ago

Converts the tall format phenotype files to the trait format needed for tassel.

The script is not quite ready but in the interest of time hoping to get a review from @MagicMilly and @rbartelme that the data is being processed correctly. The general approach is:

Average values, except leaf_desiccation_present, lodging_present, which are summed. Replace 'flowering_time', 'flag_leaf_emergence_time', 'canopy_height', 'aboveground_dry_biomass' with the values from the output from MAC_Sorghum_Data_Cleaning notebook in cyverse.

Output (as tsv): short_format_traits_season_4.txt

kshefchek commented 4 years ago

I also removed any traits where we had values for <70 culitvars, although this is arbitrary. We should use the same fields that the ML group has been using for their prototype regression models.