7baeeecd2f814ca66ab0e135f8c1cbfebfcf8763
kent
  Fri Aug 9 17:25:51 2019 -0700
Converting array operations into csv operations in preparation for making arrays operate like python string arrays more or less.

diff --git src/tabFile/tabToTabDir/tests/spec.txt src/tabFile/tabToTabDir/tests/spec.txt
index 89d1ac7..005dea8 100644
--- src/tabFile/tabToTabDir/tests/spec.txt
+++ src/tabFile/tabToTabDir/tests/spec.txt
@@ -1,50 +1,50 @@
 table a_strex_test id
 id "constant ID"
-array0 GEO_Series_summary[0]
-array1 GEO_Series_summary[1]
-array2 GEO_Series_summary[2]
+array0 uncsv(GEO_Series_summary,0)
+array1 uncsv(GEO_Series_summary,1)
+array2 uncsv(GEO_Series_summary,2)
 mm	separate(submission_date, '-', 1)
 dd	separate(submission_date, '-', 2)
 yyyy	separate(submission_date, '-', 0)
 usaDate separate(submission_date, '-', 1) + '/' + separate(submission_date, '-', 2) + '/' + separate(submission_date, '-', 0)
 company split(fluidics_chip, 0)
 md5.sum md5(GEO_Series_summary)
 organ trim(between('human', title, 'transcriptome'))
 untrimmed_organ "'" + between('human', title, 'transcriptome') + "'"
 
 table project id
 id data_set_id
 title	
 lab	lab
 submitter
 
 table donor biosample_source_id
 biosample_source_id
 species
 biosample_source_gender 
 biosample_source_age biosample_source_age_value
 biosample_source_age_unit
 # GEO_Sample_age looks like:  prenatal 16-18 W
 geo_age split(GEO_Sample_age, 1)
 geo_age_unit split(GEO_Sample_age, 2)
 geo_life_stage split(GEO_Sample_age, 0)
 project	@project
 
 table specimen id
 id 	biosample_source_id + ' ' + split(sample_label, 0) + ' ' + split(sample_label, 1) + ' ' + split(sample_label, 2)
 donor	@donor
 organ	"brain"
 tissue 	split(sample_label, 0) + ' ' + split(sample_label, 1) + ' ' + split(sample_label, 2)
 
 table fluidics_chip id
 id lab_quake_fluidics_chip
 specimen @specimen
 
 table sample id
 fluidics_chip @fluidics_chip
 specimen @specimen
 donor @donor
 id ncbi_bio_sample
 biosample_cell_type
 lab_quake_cell