d85e73c10264f168a856e4fbebca929fb9cf4f0c
kent
  Sun Aug 11 10:30:41 2019 -0700
Updating test set with replace function.

diff --git src/tabFile/tabToTabDir/tests/spec.txt src/tabFile/tabToTabDir/tests/spec.txt
index f5e9e66..4048845 100644
--- src/tabFile/tabToTabDir/tests/spec.txt
+++ src/tabFile/tabToTabDir/tests/spec.txt
@@ -1,64 +1,67 @@
 table a_strex_test id
 id "constant ID"
 #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)
 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)
 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