61880e9a394d1eb8416c8b8f3396fc4a0f7a372a
kent
  Fri Aug 23 21:15:17 2019 -0700
Adjusting test set to builtin function name changes.

diff --git src/tabFile/tabToTabDir/tests/input/spec.txt src/tabFile/tabToTabDir/tests/input/spec.txt
index 665b121..ff1ffde 100644
--- src/tabFile/tabToTabDir/tests/input/spec.txt
+++ src/tabFile/tabToTabDir/tests/input/spec.txt
@@ -1,99 +1,99 @@
 define
 messy	"big messy string messy very messy with many messy parts"
 tidy    "tidy string"
-complex	split(messy,4)
+complex	word(messy,4)
 
 table var_test id
 x	complex + " complex"
 id	tidy
 less_messy tidy("messy ", messy, " very")
 mangled_date	symbol("DATE_", submission_date)
 messy	messy
 
 table a_strex_test id
 tooLoud warn("this is a test of the warning system")
 untidy "big messy string with messy parts"
 tidyStart tidy("messy ", "big messy string with messy parts", "")
 tidyEnd tidy("", "big messy string with messy parts", " messy")
 tidyBoth tidy("messy ", "big messy string with messy parts", " messy")
 yes ( same("a", "a") ? "yes" : "no")
 no ( same("a", "b") ? "yes" : "no")
-cond ( ends("abc", "d") ? "D is cond" : ends("abc", "b") ? "B is cond" : ends("abc", "c") ? "C is cond" : "unmatched")
+cond ( ends_with("abc", "d") ? "D is cond" : ends_with("abc", "b") ? "B is cond" : ends_with("abc", "c") ? "C is cond" : "unmatched")
 id "constant ID"
 symboled symbol("ID_", "constant ID")
 pickedNum pick( 0? 0:"zero", 1:"one")
 pickedString pick("a"? "b": "beta", "a": "alpha")
 lowered lower("NotMixedCase")
 uppered upper("NotMixedCase")
 stripped strip("constant ID", " aeiou")
-sub_day_of_month	separate(submission_date, '-', 2)
-neg_day_of_month  separate(submission_date, '-', -1)
-last_word split("constant ID", -1)
-penultimate_word split("constant ID", -2)
+sub_day_of_month	chop(submission_date, '-', 2)
+neg_day_of_month  chop(submission_date, '-', -1)
+last_word word("constant ID", -1)
+penultimate_word word("constant ID", -2)
 replaceSomething replace("something", "", "default value")
 replaceNothing replace("", "", "default value")
 #assay long-RNA-seq
 dashed assay[4:-3]
 long assay[:4]
 q assay[-1]
 RNA assay[5:8]
 seq assay[-3:]
 se assay[-3:-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)
+mm	chop(submission_date, '-', 1)
+dd	chop(submission_date, '-', 2)
+yyyy	chop(submission_date, '-', 0)
+usaDate chop(submission_date, '-', 1) + '/' + chop(submission_date, '-', 2) + '/' + chop(submission_date, '-', 0)
+company word(fluidics_chip, 0)
 md5.sum md5(GEO_Series_summary)
 organ trim(between('human', title, 'transcriptome'))
 untrimmed_organ "'" + between('human', title, 'transcriptome') + "'"
 alphabet3 "abcdefg"[3]
 decade submission_date[2]
 crasho 1[1]
 abc "abcdefg"
 def "abcdefg"[3:6]
 abcd "abcdefg"[:4]
 efg "abcdefg"[4:]
 atoG "abcdefg"[:]
 fg "abcdefg"[-2:]
 array1 uncsv(GEO_Series_summary,1)
 cutMid replace("abcdefg", "cde", "")
 subSub replace("abcdefg", "abcdefg", "subSub")
 
 
 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)
+geo_age word(GEO_Sample_age, 1)
+geo_age_unit word(GEO_Sample_age, 2)
+geo_life_stage word(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)
+id 	biosample_source_id + ' ' + word(sample_label, 0) + ' ' + word(sample_label, 1) + ' ' + word(sample_label, 2)
 donor	@donor
 organ	"brain"
-tissue 	split(sample_label, 0) + ' ' + split(sample_label, 1) + ' ' + split(sample_label, 2)
+tissue 	word(sample_label, 0) + ' ' + word(sample_label, 1) + ' ' + word(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