bio-ucsc-api 0.2.0 → 0.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.rdoc +79 -47
- data/Rakefile +4 -2
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +408 -3
- data/lib/bio-ucsc.rb +162 -8
- data/lib/bio-ucsc/ailmel1.rb +21 -0
- data/lib/bio-ucsc/ailmel1/db_connection.rb +57 -0
- data/lib/bio-ucsc/anocar2.rb +22 -0
- data/lib/bio-ucsc/anocar2/db_connection.rb +57 -0
- data/lib/bio-ucsc/anogam1.rb +30 -0
- data/lib/bio-ucsc/anogam1/chaindm3.rb +81 -0
- data/lib/bio-ucsc/anogam1/chaindm3link.rb +81 -0
- data/lib/bio-ucsc/anogam1/db_connection.rb +57 -0
- data/lib/bio-ucsc/anogam1/est.rb +81 -0
- data/lib/bio-ucsc/anogam1/gap.rb +81 -0
- data/lib/bio-ucsc/anogam1/gold.rb +81 -0
- data/lib/bio-ucsc/anogam1/intronest.rb +81 -0
- data/lib/bio-ucsc/anogam1/mrna.rb +81 -0
- data/lib/bio-ucsc/anogam1/rmsk.rb +78 -0
- data/lib/bio-ucsc/apimel2.rb +26 -0
- data/lib/bio-ucsc/apimel2/chaindm2.rb +81 -0
- data/lib/bio-ucsc/apimel2/chaindm2link.rb +81 -0
- data/lib/bio-ucsc/apimel2/db_connection.rb +57 -0
- data/lib/bio-ucsc/aplcal1.rb +33 -0
- data/lib/bio-ucsc/aplcal1/chaincaepb1.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaincaepb1link.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaincaerem2.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaincaerem2link.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaincb3.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaincb3link.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaince6.rb +81 -0
- data/lib/bio-ucsc/aplcal1/chaince6link.rb +81 -0
- data/lib/bio-ucsc/aplcal1/db_connection.rb +57 -0
- data/lib/bio-ucsc/aplcal1/gap.rb +81 -0
- data/lib/bio-ucsc/aplcal1/gold.rb +81 -0
- data/lib/bio-ucsc/aplcal1/rmsk.rb +78 -0
- data/lib/bio-ucsc/bostau4.rb +24 -0
- data/lib/bio-ucsc/bostau4/db_connection.rb +57 -0
- data/lib/bio-ucsc/braflo1.rb +32 -0
- data/lib/bio-ucsc/braflo1/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/braflo1/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainhg18.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainhg18link.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainmm9.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainpetmar1.rb +81 -0
- data/lib/bio-ucsc/braflo1/chainpetmar1link.rb +81 -0
- data/lib/bio-ucsc/braflo1/db_connection.rb +57 -0
- data/lib/bio-ucsc/braflo1/gap.rb +81 -0
- data/lib/bio-ucsc/braflo1/gold.rb +81 -0
- data/lib/bio-ucsc/caejap1.rb +26 -0
- data/lib/bio-ucsc/caejap1/chaince6.rb +81 -0
- data/lib/bio-ucsc/caejap1/chaince6link.rb +81 -0
- data/lib/bio-ucsc/caejap1/db_connection.rb +57 -0
- data/lib/bio-ucsc/caejap1/gap.rb +81 -0
- data/lib/bio-ucsc/caejap1/gold.rb +81 -0
- data/lib/bio-ucsc/caepb2.rb +26 -0
- data/lib/bio-ucsc/caepb2/chaince6.rb +81 -0
- data/lib/bio-ucsc/caepb2/chaince6link.rb +81 -0
- data/lib/bio-ucsc/caepb2/db_connection.rb +57 -0
- data/lib/bio-ucsc/caepb2/gap.rb +81 -0
- data/lib/bio-ucsc/caepb2/gold.rb +81 -0
- data/lib/bio-ucsc/caerem3.rb +26 -0
- data/lib/bio-ucsc/caerem3/chaince6.rb +81 -0
- data/lib/bio-ucsc/caerem3/chaince6link.rb +81 -0
- data/lib/bio-ucsc/caerem3/db_connection.rb +57 -0
- data/lib/bio-ucsc/caerem3/gap.rb +81 -0
- data/lib/bio-ucsc/caerem3/gold.rb +81 -0
- data/lib/bio-ucsc/caljac3.rb +24 -0
- data/lib/bio-ucsc/caljac3/db_connection.rb +55 -0
- data/lib/bio-ucsc/canfam2.rb +39 -0
- data/lib/bio-ucsc/canfam2/chainbostau4.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainbostau4link.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainmm9.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainrn4.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainrn4link.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainself.rb +81 -0
- data/lib/bio-ucsc/canfam2/chainselflink.rb +81 -0
- data/lib/bio-ucsc/canfam2/db_connection.rb +57 -0
- data/lib/bio-ucsc/canfam2/est.rb +81 -0
- data/lib/bio-ucsc/canfam2/gap.rb +81 -0
- data/lib/bio-ucsc/canfam2/gold.rb +81 -0
- data/lib/bio-ucsc/canfam2/intronest.rb +81 -0
- data/lib/bio-ucsc/canfam2/mrna.rb +81 -0
- data/lib/bio-ucsc/canfam2/rmsk.rb +78 -0
- data/lib/bio-ucsc/cavpor3.rb +21 -0
- data/lib/bio-ucsc/cavpor3/db_connection.rb +57 -0
- data/lib/bio-ucsc/cb3.rb +36 -0
- data/lib/bio-ucsc/cb3/chaincaepb1.rb +81 -0
- data/lib/bio-ucsc/cb3/chaincaepb1link.rb +81 -0
- data/lib/bio-ucsc/cb3/chaincaerem2.rb +81 -0
- data/lib/bio-ucsc/cb3/chaincaerem2link.rb +81 -0
- data/lib/bio-ucsc/cb3/chaince6.rb +81 -0
- data/lib/bio-ucsc/cb3/chaince6link.rb +81 -0
- data/lib/bio-ucsc/cb3/chainpripac1.rb +81 -0
- data/lib/bio-ucsc/cb3/chainpripac1link.rb +81 -0
- data/lib/bio-ucsc/cb3/db_connection.rb +57 -0
- data/lib/bio-ucsc/cb3/est.rb +81 -0
- data/lib/bio-ucsc/cb3/gap.rb +81 -0
- data/lib/bio-ucsc/cb3/gold.rb +81 -0
- data/lib/bio-ucsc/cb3/intronest.rb +81 -0
- data/lib/bio-ucsc/cb3/mrna.rb +81 -0
- data/lib/bio-ucsc/cb3/rmsk.rb +78 -0
- data/lib/bio-ucsc/ce6/chaincaejap1.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincaejap1link.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincaepb2.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincaepb2link.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincaerem3.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincaerem3link.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincb3.rb +2 -2
- data/lib/bio-ucsc/ce6/chaincb3link.rb +2 -2
- data/lib/bio-ucsc/ce6/chainpripac1.rb +2 -2
- data/lib/bio-ucsc/ce6/chainpripac1link.rb +2 -2
- data/lib/bio-ucsc/ce6/chainself.rb +2 -2
- data/lib/bio-ucsc/ce6/chainselflink.rb +2 -2
- data/lib/bio-ucsc/ce6/db_connection.rb +5 -6
- data/lib/bio-ucsc/ce6/est.rb +2 -2
- data/lib/bio-ucsc/ce6/gap.rb +2 -2
- data/lib/bio-ucsc/ce6/gold.rb +2 -2
- data/lib/bio-ucsc/ce6/intronest.rb +2 -2
- data/lib/bio-ucsc/ce6/mrna.rb +2 -2
- data/lib/bio-ucsc/ce6/rmsk.rb +2 -2
- data/lib/bio-ucsc/ce6/t25mersrepeats.rb +2 -2
- data/lib/bio-ucsc/ci2.rb +23 -0
- data/lib/bio-ucsc/ci2/db_connection.rb +55 -0
- data/lib/bio-ucsc/danrer7.rb +24 -0
- data/lib/bio-ucsc/danrer7/db_connection.rb +57 -0
- data/lib/bio-ucsc/dm3/chainanogam1.rb +2 -2
- data/lib/bio-ucsc/dm3/chainanogam1link.rb +2 -2
- data/lib/bio-ucsc/dm3/chainapimel3.rb +2 -2
- data/lib/bio-ucsc/dm3/chainapimel3link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindp3.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindp3link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroana2.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroana2link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroere1.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroere1link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroper1.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroper1link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindrosec1.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindrosec1link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindrosim1.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindrosim1link.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroyak2.rb +2 -2
- data/lib/bio-ucsc/dm3/chaindroyak2link.rb +2 -2
- data/lib/bio-ucsc/dm3/db_connection.rb +5 -6
- data/lib/bio-ucsc/dm3/est.rb +2 -2
- data/lib/bio-ucsc/dm3/gap.rb +2 -2
- data/lib/bio-ucsc/dm3/gold.rb +2 -2
- data/lib/bio-ucsc/dm3/intronest.rb +2 -2
- data/lib/bio-ucsc/dm3/mrna.rb +2 -2
- data/lib/bio-ucsc/dm3/rmsk.rb +2 -2
- data/lib/bio-ucsc/dp3.rb +33 -0
- data/lib/bio-ucsc/dp3/chaindm3.rb +81 -0
- data/lib/bio-ucsc/dp3/chaindm3link.rb +81 -0
- data/lib/bio-ucsc/dp3/db_connection.rb +57 -0
- data/lib/bio-ucsc/dp3/est.rb +81 -0
- data/lib/bio-ucsc/dp3/gap.rb +81 -0
- data/lib/bio-ucsc/dp3/gold.rb +81 -0
- data/lib/bio-ucsc/dp3/intronest.rb +81 -0
- data/lib/bio-ucsc/dp3/mrna.rb +81 -0
- data/lib/bio-ucsc/dp3/rmsk.rb +78 -0
- data/lib/bio-ucsc/droana2.rb +22 -0
- data/lib/bio-ucsc/droana2/db_connection.rb +57 -0
- data/lib/bio-ucsc/droere1.rb +22 -0
- data/lib/bio-ucsc/droere1/db_connection.rb +57 -0
- data/lib/bio-ucsc/drogri1.rb +22 -0
- data/lib/bio-ucsc/drogri1/db_connection.rb +57 -0
- data/lib/bio-ucsc/dromoj2.rb +22 -0
- data/lib/bio-ucsc/dromoj2/db_connection.rb +57 -0
- data/lib/bio-ucsc/droper1.rb +22 -0
- data/lib/bio-ucsc/droper1/db_connection.rb +57 -0
- data/lib/bio-ucsc/drosec1.rb +22 -0
- data/lib/bio-ucsc/drosec1/db_connection.rb +57 -0
- data/lib/bio-ucsc/drosim1.rb +30 -0
- data/lib/bio-ucsc/drosim1/chaindm3.rb +81 -0
- data/lib/bio-ucsc/drosim1/chaindm3link.rb +81 -0
- data/lib/bio-ucsc/drosim1/db_connection.rb +57 -0
- data/lib/bio-ucsc/drosim1/est.rb +81 -0
- data/lib/bio-ucsc/drosim1/gap.rb +81 -0
- data/lib/bio-ucsc/drosim1/gold.rb +81 -0
- data/lib/bio-ucsc/drosim1/intronest.rb +81 -0
- data/lib/bio-ucsc/drosim1/mrna.rb +81 -0
- data/lib/bio-ucsc/drosim1/rmsk.rb +78 -0
- data/lib/bio-ucsc/drovir2.rb +22 -0
- data/lib/bio-ucsc/drovir2/db_connection.rb +57 -0
- data/lib/bio-ucsc/droyak2.rb +32 -0
- data/lib/bio-ucsc/droyak2/chaindm3.rb +81 -0
- data/lib/bio-ucsc/droyak2/chaindm3link.rb +81 -0
- data/lib/bio-ucsc/droyak2/db_connection.rb +57 -0
- data/lib/bio-ucsc/droyak2/est.rb +81 -0
- data/lib/bio-ucsc/droyak2/gap.rb +81 -0
- data/lib/bio-ucsc/droyak2/gold.rb +81 -0
- data/lib/bio-ucsc/droyak2/intronest.rb +81 -0
- data/lib/bio-ucsc/droyak2/mrna.rb +81 -0
- data/lib/bio-ucsc/droyak2/rmsk.rb +78 -0
- data/lib/bio-ucsc/equcab2.rb +31 -0
- data/lib/bio-ucsc/equcab2/db_connection.rb +57 -0
- data/lib/bio-ucsc/equcab2/est.rb +81 -0
- data/lib/bio-ucsc/equcab2/gap.rb +81 -0
- data/lib/bio-ucsc/equcab2/gold.rb +81 -0
- data/lib/bio-ucsc/equcab2/intronest.rb +81 -0
- data/lib/bio-ucsc/equcab2/mrna.rb +81 -0
- data/lib/bio-ucsc/equcab2/rmsk.rb +78 -0
- data/lib/bio-ucsc/felcat4.rb +23 -0
- data/lib/bio-ucsc/felcat4/db_connection.rb +57 -0
- data/lib/bio-ucsc/fr2.rb +35 -0
- data/lib/bio-ucsc/fr2/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/fr2/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/fr2/chaingasacu1.rb +81 -0
- data/lib/bio-ucsc/fr2/chaingasacu1link.rb +81 -0
- data/lib/bio-ucsc/fr2/chainmm9.rb +81 -0
- data/lib/bio-ucsc/fr2/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/fr2/chainorylat2.rb +81 -0
- data/lib/bio-ucsc/fr2/chainorylat2link.rb +81 -0
- data/lib/bio-ucsc/fr2/db_connection.rb +57 -0
- data/lib/bio-ucsc/fr2/est.rb +81 -0
- data/lib/bio-ucsc/fr2/gap.rb +81 -0
- data/lib/bio-ucsc/fr2/gold.rb +81 -0
- data/lib/bio-ucsc/fr2/intronest.rb +81 -0
- data/lib/bio-ucsc/fr2/mrna.rb +81 -0
- data/lib/bio-ucsc/fr2/rmsk.rb +78 -0
- data/lib/bio-ucsc/galgal3.rb +54 -0
- data/lib/bio-ucsc/galgal3/chainanocar1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainanocar1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainbraflo1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainbraflo1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaincavpor3.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaincavpor3link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaindanrer4.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaindanrer4link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainfr2.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainfr2link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaingasacu1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaingasacu1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainmm9.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainornana1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainornana1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainpetmar1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainpetmar1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainrn4.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainrn4link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaintaegut1.rb +81 -0
- data/lib/bio-ucsc/galgal3/chaintaegut1link.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainxentro2.rb +81 -0
- data/lib/bio-ucsc/galgal3/chainxentro2link.rb +81 -0
- data/lib/bio-ucsc/galgal3/db_connection.rb +57 -0
- data/lib/bio-ucsc/galgal3/est.rb +81 -0
- data/lib/bio-ucsc/galgal3/gap.rb +81 -0
- data/lib/bio-ucsc/galgal3/gold.rb +81 -0
- data/lib/bio-ucsc/galgal3/intronest.rb +81 -0
- data/lib/bio-ucsc/galgal3/mrna.rb +81 -0
- data/lib/bio-ucsc/galgal3/rmsk.rb +78 -0
- data/lib/bio-ucsc/gasacu1.rb +39 -0
- data/lib/bio-ucsc/gasacu1/chainanocar1.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainanocar1link.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainfr2.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainfr2link.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainmm9.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainorylat2.rb +81 -0
- data/lib/bio-ucsc/gasacu1/chainorylat2link.rb +81 -0
- data/lib/bio-ucsc/gasacu1/db_connection.rb +57 -0
- data/lib/bio-ucsc/gasacu1/est.rb +81 -0
- data/lib/bio-ucsc/gasacu1/intronest.rb +81 -0
- data/lib/bio-ucsc/gasacu1/mrna.rb +81 -0
- data/lib/bio-ucsc/gasacu1/rmsk.rb +78 -0
- data/lib/bio-ucsc/go/db_connection.rb +5 -6
- data/lib/bio-ucsc/hg18/chainanocar1.rb +2 -2
- data/lib/bio-ucsc/hg18/chainbostau4.rb +2 -2
- data/lib/bio-ucsc/hg18/chainbraflo1.rb +2 -2
- data/lib/bio-ucsc/hg18/chaincaljac1.rb +2 -2
- data/lib/bio-ucsc/hg18/chaincanfam2.rb +2 -2
- data/lib/bio-ucsc/hg18/chaincavpor3.rb +2 -2
- data/lib/bio-ucsc/hg18/chaindanrer5.rb +2 -2
- data/lib/bio-ucsc/hg18/chainequcab1.rb +2 -2
- data/lib/bio-ucsc/hg18/chainfelcat3.rb +2 -2
- data/lib/bio-ucsc/hg18/chainfr2.rb +2 -2
- data/lib/bio-ucsc/hg18/chaingalgal3.rb +2 -2
- data/lib/bio-ucsc/hg18/chaingasacu1.rb +2 -2
- data/lib/bio-ucsc/hg18/chainmm9.rb +2 -2
- data/lib/bio-ucsc/hg18/chainmondom4.rb +2 -2
- data/lib/bio-ucsc/hg18/chainornana1.rb +2 -2
- data/lib/bio-ucsc/hg18/chainorylat2.rb +2 -2
- data/lib/bio-ucsc/hg18/chainpantro2.rb +2 -2
- data/lib/bio-ucsc/hg18/chainpetmar1.rb +2 -2
- data/lib/bio-ucsc/hg18/chainponabe2.rb +2 -2
- data/lib/bio-ucsc/hg18/chainrhemac2.rb +2 -2
- data/lib/bio-ucsc/hg18/chainrn4.rb +2 -2
- data/lib/bio-ucsc/hg18/chainself.rb +2 -2
- data/lib/bio-ucsc/hg18/chainstrpur2.rb +2 -2
- data/lib/bio-ucsc/hg18/chaintaegut1.rb +2 -2
- data/lib/bio-ucsc/hg18/chaintetnig2.rb +2 -2
- data/lib/bio-ucsc/hg18/chainxentro2.rb +2 -2
- data/lib/bio-ucsc/hg18/db_connection.rb +5 -7
- data/lib/bio-ucsc/hg18/gap.rb +2 -2
- data/lib/bio-ucsc/hg18/gold.rb +2 -2
- data/lib/bio-ucsc/hg18/intronest.rb +2 -2
- data/lib/bio-ucsc/hg18/rmsk.rb +2 -2
- data/lib/bio-ucsc/hg18/rmskrm327.rb +2 -2
- data/lib/bio-ucsc/hgfixed/db_connection.rb +5 -6
- data/lib/bio-ucsc/loxafr3.rb +20 -0
- data/lib/bio-ucsc/loxafr3/db_connection.rb +57 -0
- data/lib/bio-ucsc/mm9/chainanocar1.rb +2 -2
- data/lib/bio-ucsc/mm9/chainanocar1link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainbostau4.rb +2 -2
- data/lib/bio-ucsc/mm9/chainbostau4link.rb +3 -3
- data/lib/bio-ucsc/mm9/chainbraflo1.rb +2 -2
- data/lib/bio-ucsc/mm9/chainbraflo1link.rb +2 -2
- data/lib/bio-ucsc/mm9/chaincanfam2.rb +2 -2
- data/lib/bio-ucsc/mm9/chaincanfam2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chaincavpor3.rb +2 -2
- data/lib/bio-ucsc/mm9/chaincavpor3link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainfr2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainfr2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chaingalgal3.rb +2 -2
- data/lib/bio-ucsc/mm9/chaingalgal3link.rb +2 -2
- data/lib/bio-ucsc/mm9/chaingasacu1.rb +2 -2
- data/lib/bio-ucsc/mm9/chaingasacu1link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainornana1.rb +2 -2
- data/lib/bio-ucsc/mm9/chainornana1link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainorylat2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainorylat2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainpantro2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainpantro2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainpetmar1.rb +2 -2
- data/lib/bio-ucsc/mm9/chainpetmar1link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainponabe2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainponabe2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainrhemac2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainrhemac2link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainrn4.rb +2 -2
- data/lib/bio-ucsc/mm9/chainrn4link.rb +2 -2
- data/lib/bio-ucsc/mm9/chainxentro2.rb +2 -2
- data/lib/bio-ucsc/mm9/chainxentro2link.rb +2 -2
- data/lib/bio-ucsc/mm9/db_connection.rb +6 -7
- data/lib/bio-ucsc/mm9/est.rb +2 -2
- data/lib/bio-ucsc/mm9/gap.rb +2 -2
- data/lib/bio-ucsc/mm9/gold.rb +2 -2
- data/lib/bio-ucsc/mm9/intronest.rb +2 -2
- data/lib/bio-ucsc/mm9/mrna.rb +2 -2
- data/lib/bio-ucsc/mm9/rmsk.rb +2 -2
- data/lib/bio-ucsc/mondom5.rb +21 -0
- data/lib/bio-ucsc/mondom5/db_connection.rb +57 -0
- data/lib/bio-ucsc/ornana1.rb +20 -0
- data/lib/bio-ucsc/ornana1/db_connection.rb +57 -0
- data/lib/bio-ucsc/orycun2.rb +24 -0
- data/lib/bio-ucsc/orycun2/db_connection.rb +57 -0
- data/lib/bio-ucsc/orylat2.rb +24 -0
- data/lib/bio-ucsc/orylat2/db_connection.rb +55 -0
- data/lib/bio-ucsc/oviari1.rb +24 -0
- data/lib/bio-ucsc/oviari1/db_connection.rb +57 -0
- data/lib/bio-ucsc/pantro3.rb +24 -0
- data/lib/bio-ucsc/pantro3/db_connection.rb +55 -0
- data/lib/bio-ucsc/petmar1.rb +22 -0
- data/lib/bio-ucsc/petmar1/db_connection.rb +57 -0
- data/lib/bio-ucsc/ponabe2.rb +36 -0
- data/lib/bio-ucsc/ponabe2/chainmm9.rb +81 -0
- data/lib/bio-ucsc/ponabe2/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/ponabe2/chainornana1.rb +81 -0
- data/lib/bio-ucsc/ponabe2/chainornana1link.rb +81 -0
- data/lib/bio-ucsc/ponabe2/chainrhemac2.rb +81 -0
- data/lib/bio-ucsc/ponabe2/chainrhemac2link.rb +81 -0
- data/lib/bio-ucsc/ponabe2/db_connection.rb +55 -0
- data/lib/bio-ucsc/ponabe2/est.rb +81 -0
- data/lib/bio-ucsc/ponabe2/gap.rb +81 -0
- data/lib/bio-ucsc/ponabe2/gold.rb +81 -0
- data/lib/bio-ucsc/ponabe2/intronest.rb +81 -0
- data/lib/bio-ucsc/ponabe2/mrna.rb +81 -0
- data/lib/bio-ucsc/ponabe2/rmsk.rb +78 -0
- data/lib/bio-ucsc/pripac1.rb +33 -0
- data/lib/bio-ucsc/pripac1/chaincaepb1.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaincaepb1link.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaincaerem2.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaincaerem2link.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaincb3.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaincb3link.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaince6.rb +81 -0
- data/lib/bio-ucsc/pripac1/chaince6link.rb +81 -0
- data/lib/bio-ucsc/pripac1/db_connection.rb +57 -0
- data/lib/bio-ucsc/pripac1/gap.rb +81 -0
- data/lib/bio-ucsc/pripac1/gold.rb +81 -0
- data/lib/bio-ucsc/pripac1/rmsk.rb +78 -0
- data/lib/bio-ucsc/proteome/db_connection.rb +5 -7
- data/lib/bio-ucsc/rhemac2.rb +32 -0
- data/lib/bio-ucsc/rhemac2/chainmm9.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainpantro2.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainpantro2link.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainponabe2.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainponabe2link.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainrn4.rb +81 -0
- data/lib/bio-ucsc/rhemac2/chainrn4link.rb +81 -0
- data/lib/bio-ucsc/rhemac2/db_connection.rb +55 -0
- data/lib/bio-ucsc/rn4.rb +52 -0
- data/lib/bio-ucsc/rn4/chainbostau3.rb +79 -0
- data/lib/bio-ucsc/rn4/chainbostau3link.rb +79 -0
- data/lib/bio-ucsc/rn4/chaincanfam2.rb +82 -0
- data/lib/bio-ucsc/rn4/chaincanfam2link.rb +82 -0
- data/lib/bio-ucsc/rn4/chaincavpor3.rb +81 -0
- data/lib/bio-ucsc/rn4/chaincavpor3link.rb +81 -0
- data/lib/bio-ucsc/rn4/chaindanrer4.rb +81 -0
- data/lib/bio-ucsc/rn4/chaindanrer4link.rb +81 -0
- data/lib/bio-ucsc/rn4/chainequcab1.rb +81 -0
- data/lib/bio-ucsc/rn4/chainequcab1link.rb +81 -0
- data/lib/bio-ucsc/rn4/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/rn4/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/rn4/chainmm9.rb +81 -0
- data/lib/bio-ucsc/rn4/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/rn4/chainmondom4.rb +81 -0
- data/lib/bio-ucsc/rn4/chainmondom4link.rb +81 -0
- data/lib/bio-ucsc/rn4/chainpantro2.rb +81 -0
- data/lib/bio-ucsc/rn4/chainpantro2link.rb +82 -0
- data/lib/bio-ucsc/rn4/chainrhemac2.rb +81 -0
- data/lib/bio-ucsc/rn4/chainrhemac2link.rb +81 -0
- data/lib/bio-ucsc/rn4/chainxentro2.rb +81 -0
- data/lib/bio-ucsc/rn4/chainxentro2link.rb +81 -0
- data/lib/bio-ucsc/rn4/db_connection.rb +55 -0
- data/lib/bio-ucsc/rn4/est.rb +81 -0
- data/lib/bio-ucsc/rn4/gap.rb +81 -0
- data/lib/bio-ucsc/rn4/gold.rb +81 -0
- data/lib/bio-ucsc/rn4/intronest.rb +81 -0
- data/lib/bio-ucsc/rn4/mrna.rb +81 -0
- data/lib/bio-ucsc/rn4/rmsk.rb +78 -0
- data/lib/bio-ucsc/saccer2.rb +33 -0
- data/lib/bio-ucsc/saccer2/db_connection.rb +55 -0
- data/lib/bio-ucsc/saccer2/est.rb +83 -0
- data/lib/bio-ucsc/saccer2/gap.rb +83 -0
- data/lib/bio-ucsc/saccer2/gold.rb +83 -0
- data/lib/bio-ucsc/saccer2/intronest.rb +83 -0
- data/lib/bio-ucsc/saccer2/mrna.rb +83 -0
- data/lib/bio-ucsc/saccer2/t2micron_est.rb +57 -0
- data/lib/bio-ucsc/saccer2/t2micron_gap.rb +57 -0
- data/lib/bio-ucsc/saccer2/t2micron_gold.rb +58 -0
- data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb +57 -0
- data/lib/bio-ucsc/saccer2/t2micron_mrna.rb +57 -0
- data/lib/bio-ucsc/strpur2.rb +32 -0
- data/lib/bio-ucsc/strpur2/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/strpur2/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainhg18.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainhg18link.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainmm9.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainmm9link.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainpetmar1.rb +81 -0
- data/lib/bio-ucsc/strpur2/chainpetmar1link.rb +81 -0
- data/lib/bio-ucsc/strpur2/db_connection.rb +57 -0
- data/lib/bio-ucsc/strpur2/gap.rb +81 -0
- data/lib/bio-ucsc/strpur2/gold.rb +81 -0
- data/lib/bio-ucsc/susscr2.rb +26 -0
- data/lib/bio-ucsc/susscr2/db_connection.rb +57 -0
- data/lib/bio-ucsc/susscr2/est.rb +81 -0
- data/lib/bio-ucsc/susscr2/intronest.rb +81 -0
- data/lib/bio-ucsc/susscr2/mrna.rb +81 -0
- data/lib/bio-ucsc/table_class_detector.rb +18 -22
- data/lib/bio-ucsc/taegut1.rb +33 -0
- data/lib/bio-ucsc/taegut1/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/taegut1/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/taegut1/db_connection.rb +57 -0
- data/lib/bio-ucsc/taegut1/est.rb +81 -0
- data/lib/bio-ucsc/taegut1/gap.rb +81 -0
- data/lib/bio-ucsc/taegut1/gold.rb +81 -0
- data/lib/bio-ucsc/taegut1/intronest.rb +81 -0
- data/lib/bio-ucsc/taegut1/mrna.rb +81 -0
- data/lib/bio-ucsc/taegut1/rmsk.rb +78 -0
- data/lib/bio-ucsc/tetnig2.rb +25 -0
- data/lib/bio-ucsc/tetnig2/db_connection.rb +57 -0
- data/lib/bio-ucsc/tetnig2/mrna.rb +81 -0
- data/lib/bio-ucsc/uniprot/db_connection.rb +5 -7
- data/lib/bio-ucsc/visigene/db_connection.rb +5 -6
- data/lib/bio-ucsc/xentro2.rb +30 -0
- data/lib/bio-ucsc/xentro2/chaingalgal3.rb +81 -0
- data/lib/bio-ucsc/xentro2/chaingalgal3link.rb +81 -0
- data/lib/bio-ucsc/xentro2/db_connection.rb +57 -0
- data/lib/bio-ucsc/xentro2/est.rb +81 -0
- data/lib/bio-ucsc/xentro2/gap.rb +81 -0
- data/lib/bio-ucsc/xentro2/gold.rb +81 -0
- data/lib/bio-ucsc/xentro2/intronest.rb +81 -0
- data/lib/bio-ucsc/xentro2/mrna.rb +81 -0
- data/lib/bio-ucsc/xentro2/rmsk.rb +78 -0
- data/samples/hg19-2bit-retrieve.rb +5 -2
- data/spec/ailmel1_spec.rb +770 -0
- data/spec/anocar2_spec.rb +750 -0
- data/spec/anogam1_spec.rb +568 -0
- data/spec/apimel2_spec.rb +542 -0
- data/spec/aplcal1_spec.rb +530 -0
- data/spec/bostau4_spec.rb +920 -0
- data/spec/braflo1_spec.rb +660 -0
- data/spec/caejap1_spec.rb +524 -0
- data/spec/caepb2_spec.rb +515 -0
- data/spec/caerem3_spec.rb +524 -0
- data/spec/caljac3_spec.rb +860 -0
- data/spec/canfam2_spec.rb +1145 -0
- data/spec/cavpor3_spec.rb +880 -0
- data/spec/cb3_spec.rb +634 -0
- data/spec/ci2_spec.rb +520 -0
- data/spec/danrer7_spec.rb +810 -0
- data/spec/dp3_spec.rb +617 -0
- data/spec/droana2_spec.rb +500 -0
- data/spec/droere1_spec.rb +510 -0
- data/spec/drogri1_spec.rb +470 -0
- data/spec/dromoj2_spec.rb +510 -0
- data/spec/droper1_spec.rb +470 -0
- data/spec/drosec1_spec.rb +470 -0
- data/spec/drosim1_spec.rb +588 -0
- data/spec/drovir2_spec.rb +540 -0
- data/spec/droyak2_spec.rb +558 -0
- data/spec/equcab2_spec.rb +936 -0
- data/spec/felcat4_spec.rb +770 -0
- data/spec/fr2_spec.rb +835 -0
- data/spec/galgal3_spec.rb +1351 -0
- data/spec/gasacu1_spec.rb +924 -0
- data/spec/loxafr3_spec.rb +550 -0
- data/spec/mondom5_spec.rb +1230 -0
- data/spec/ornana1_spec.rb +980 -0
- data/spec/orycun2_spec.rb +770 -0
- data/spec/orylat2_spec.rb +930 -0
- data/spec/oviari1_spec.rb +670 -0
- data/spec/pantro3_spec.rb +810 -0
- data/spec/petmar1_spec.rb +770 -0
- data/spec/ponabe2_spec.rb +962 -0
- data/spec/pripac1_spec.rb +621 -0
- data/spec/rhemac2_spec.rb +958 -0
- data/spec/rn4_spec.rb +2038 -0
- data/spec/saccer2_spec.rb +925 -0
- data/spec/strpur2_spec.rb +600 -0
- data/spec/susscr2_spec.rb +623 -0
- data/spec/taegut1_spec.rb +768 -0
- data/spec/tetnig2_spec.rb +721 -0
- data/spec/xentro2_spec.rb +900 -0
- metadata +477 -23
data/spec/rn4_spec.rb
ADDED
|
@@ -0,0 +1,2038 @@
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1
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require "bio-ucsc"
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2
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require "pp"
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3
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4
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describe "Bio::Ucsc::Rn4" do
|
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5
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+
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6
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before(:all) do
|
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7
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Bio::Ucsc::Rn4::DBConnection.connect
|
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8
|
+
end
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|
9
|
+
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10
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describe "Bio::Ucsc::Rn4::AffyAllExonProbes" do
|
|
11
|
+
context ".first" do
|
|
12
|
+
it 'returns the first records' do
|
|
13
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result = Bio::Ucsc::Rn4::AffyAllExonProbes.first
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14
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pp result
|
|
15
|
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result.should be_true
|
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16
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+
end
|
|
17
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+
end
|
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18
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+
end
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19
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|
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20
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describe "Bio::Ucsc::Rn4::AffyExonTissues" do
|
|
21
|
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context ".first" do
|
|
22
|
+
it 'returns the first records' do
|
|
23
|
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result = Bio::Ucsc::Rn4::AffyExonTissues.first
|
|
24
|
+
pp result
|
|
25
|
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result.should be_true
|
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26
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+
end
|
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27
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+
end
|
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28
|
+
end
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29
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|
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30
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describe "Bio::Ucsc::Rn4::AffyExonTissuesGs" do
|
|
31
|
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context ".first" do
|
|
32
|
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it 'returns the first records' do
|
|
33
|
+
result = Bio::Ucsc::Rn4::AffyExonTissuesGs.first
|
|
34
|
+
pp result
|
|
35
|
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result.should be_true
|
|
36
|
+
end
|
|
37
|
+
end
|
|
38
|
+
end
|
|
39
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+
|
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40
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describe "Bio::Ucsc::Rn4::AffyExonTissuesGsExps" do
|
|
41
|
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context ".first" do
|
|
42
|
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it 'returns the first records' do
|
|
43
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result = Bio::Ucsc::Rn4::AffyExonTissuesGsExps.first
|
|
44
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pp result
|
|
45
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result.should be_true
|
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46
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+
end
|
|
47
|
+
end
|
|
48
|
+
end
|
|
49
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+
|
|
50
|
+
describe "Bio::Ucsc::Rn4::AffyExonTissuesGsMedian" do
|
|
51
|
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context ".first" do
|
|
52
|
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it 'returns the first records' do
|
|
53
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result = Bio::Ucsc::Rn4::AffyExonTissuesGsMedian.first
|
|
54
|
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pp result
|
|
55
|
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result.should be_true
|
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56
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+
end
|
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57
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+
end
|
|
58
|
+
end
|
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59
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|
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60
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describe "Bio::Ucsc::Rn4::AffyExonTissuesGsMedianDist" do
|
|
61
|
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context ".first" do
|
|
62
|
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it 'returns the first records' do
|
|
63
|
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result = Bio::Ucsc::Rn4::AffyExonTissuesGsMedianDist.first
|
|
64
|
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pp result
|
|
65
|
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result.should be_true
|
|
66
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+
end
|
|
67
|
+
end
|
|
68
|
+
end
|
|
69
|
+
|
|
70
|
+
describe "Bio::Ucsc::Rn4::AffyExonTissuesGsMedianExps" do
|
|
71
|
+
context ".first" do
|
|
72
|
+
it 'returns the first records' do
|
|
73
|
+
result = Bio::Ucsc::Rn4::AffyExonTissuesGsMedianExps.first
|
|
74
|
+
pp result
|
|
75
|
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result.should be_true
|
|
76
|
+
end
|
|
77
|
+
end
|
|
78
|
+
end
|
|
79
|
+
|
|
80
|
+
describe "Bio::Ucsc::Rn4::AffyRAE230" do
|
|
81
|
+
context ".first" do
|
|
82
|
+
it 'returns the first records' do
|
|
83
|
+
result = Bio::Ucsc::Rn4::AffyRAE230.first
|
|
84
|
+
pp result
|
|
85
|
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result.should be_true
|
|
86
|
+
end
|
|
87
|
+
end
|
|
88
|
+
end
|
|
89
|
+
|
|
90
|
+
describe "Bio::Ucsc::Rn4::AffyU34A" do
|
|
91
|
+
context ".first" do
|
|
92
|
+
it 'returns the first records' do
|
|
93
|
+
result = Bio::Ucsc::Rn4::AffyU34A.first
|
|
94
|
+
pp result
|
|
95
|
+
result.should be_true
|
|
96
|
+
end
|
|
97
|
+
end
|
|
98
|
+
end
|
|
99
|
+
|
|
100
|
+
describe "Bio::Ucsc::Rn4::AgilentCgh105a" do
|
|
101
|
+
context ".first" do
|
|
102
|
+
it 'returns the first records' do
|
|
103
|
+
result = Bio::Ucsc::Rn4::AgilentCgh105a.first
|
|
104
|
+
pp result
|
|
105
|
+
result.should be_true
|
|
106
|
+
end
|
|
107
|
+
end
|
|
108
|
+
end
|
|
109
|
+
|
|
110
|
+
describe "Bio::Ucsc::Rn4::AgilentCgh1x1m" do
|
|
111
|
+
context ".first" do
|
|
112
|
+
it 'returns the first records' do
|
|
113
|
+
result = Bio::Ucsc::Rn4::AgilentCgh1x1m.first
|
|
114
|
+
pp result
|
|
115
|
+
result.should be_true
|
|
116
|
+
end
|
|
117
|
+
end
|
|
118
|
+
end
|
|
119
|
+
|
|
120
|
+
describe "Bio::Ucsc::Rn4::AgilentCgh244a" do
|
|
121
|
+
context ".first" do
|
|
122
|
+
it 'returns the first records' do
|
|
123
|
+
result = Bio::Ucsc::Rn4::AgilentCgh244a.first
|
|
124
|
+
pp result
|
|
125
|
+
result.should be_true
|
|
126
|
+
end
|
|
127
|
+
end
|
|
128
|
+
end
|
|
129
|
+
|
|
130
|
+
describe "Bio::Ucsc::Rn4::AgilentCgh4x180k" do
|
|
131
|
+
context ".first" do
|
|
132
|
+
it 'returns the first records' do
|
|
133
|
+
result = Bio::Ucsc::Rn4::AgilentCgh4x180k.first
|
|
134
|
+
pp result
|
|
135
|
+
result.should be_true
|
|
136
|
+
end
|
|
137
|
+
end
|
|
138
|
+
end
|
|
139
|
+
|
|
140
|
+
describe "Bio::Ucsc::Rn4::All_bacends" do
|
|
141
|
+
context ".first" do
|
|
142
|
+
it 'returns the first records' do
|
|
143
|
+
result = Bio::Ucsc::Rn4::All_bacends.first
|
|
144
|
+
pp result
|
|
145
|
+
result.should be_true
|
|
146
|
+
end
|
|
147
|
+
end
|
|
148
|
+
end
|
|
149
|
+
|
|
150
|
+
describe "Bio::Ucsc::Rn4::All_est" do
|
|
151
|
+
context ".first" do
|
|
152
|
+
it 'returns the first records' do
|
|
153
|
+
result = Bio::Ucsc::Rn4::All_est.first
|
|
154
|
+
pp result
|
|
155
|
+
result.should be_true
|
|
156
|
+
end
|
|
157
|
+
end
|
|
158
|
+
end
|
|
159
|
+
|
|
160
|
+
describe "Bio::Ucsc::Rn4::All_mrna" do
|
|
161
|
+
context ".first" do
|
|
162
|
+
it 'returns the first records' do
|
|
163
|
+
result = Bio::Ucsc::Rn4::All_mrna.first
|
|
164
|
+
pp result
|
|
165
|
+
result.should be_true
|
|
166
|
+
end
|
|
167
|
+
end
|
|
168
|
+
end
|
|
169
|
+
|
|
170
|
+
describe "Bio::Ucsc::Rn4::All_sts_primer" do
|
|
171
|
+
context ".first" do
|
|
172
|
+
it 'returns the first records' do
|
|
173
|
+
result = Bio::Ucsc::Rn4::All_sts_primer.first
|
|
174
|
+
pp result
|
|
175
|
+
result.should be_true
|
|
176
|
+
end
|
|
177
|
+
end
|
|
178
|
+
end
|
|
179
|
+
|
|
180
|
+
describe "Bio::Ucsc::Rn4::Author" do
|
|
181
|
+
context ".first" do
|
|
182
|
+
it 'returns the first records' do
|
|
183
|
+
result = Bio::Ucsc::Rn4::Author.first
|
|
184
|
+
pp result
|
|
185
|
+
result.should be_true
|
|
186
|
+
end
|
|
187
|
+
end
|
|
188
|
+
end
|
|
189
|
+
|
|
190
|
+
describe "Bio::Ucsc::Rn4::BacEndPairs" do
|
|
191
|
+
context ".first" do
|
|
192
|
+
it 'returns the first records' do
|
|
193
|
+
result = Bio::Ucsc::Rn4::BacEndPairs.first
|
|
194
|
+
pp result
|
|
195
|
+
result.should be_true
|
|
196
|
+
end
|
|
197
|
+
end
|
|
198
|
+
end
|
|
199
|
+
|
|
200
|
+
describe "Bio::Ucsc::Rn4::Cds" do
|
|
201
|
+
context ".first" do
|
|
202
|
+
it 'returns the first records' do
|
|
203
|
+
result = Bio::Ucsc::Rn4::Cds.first
|
|
204
|
+
pp result
|
|
205
|
+
result.should be_true
|
|
206
|
+
end
|
|
207
|
+
end
|
|
208
|
+
end
|
|
209
|
+
|
|
210
|
+
describe "Bio::Ucsc::Rn4::CeBlastTab" do
|
|
211
|
+
context ".first" do
|
|
212
|
+
it 'returns the first records' do
|
|
213
|
+
result = Bio::Ucsc::Rn4::CeBlastTab.first
|
|
214
|
+
pp result
|
|
215
|
+
result.should be_true
|
|
216
|
+
end
|
|
217
|
+
end
|
|
218
|
+
end
|
|
219
|
+
|
|
220
|
+
describe "Bio::Ucsc::Rn4::Cell" do
|
|
221
|
+
context ".first" do
|
|
222
|
+
it 'returns the first records' do
|
|
223
|
+
result = Bio::Ucsc::Rn4::Cell.first
|
|
224
|
+
pp result
|
|
225
|
+
result.should be_true
|
|
226
|
+
end
|
|
227
|
+
end
|
|
228
|
+
end
|
|
229
|
+
|
|
230
|
+
describe "Bio::Ucsc::Rn4::ChainAilMel1" do
|
|
231
|
+
context ".first" do
|
|
232
|
+
it 'returns the first records' do
|
|
233
|
+
result = Bio::Ucsc::Rn4::ChainAilMel1.first
|
|
234
|
+
pp result
|
|
235
|
+
result.should be_true
|
|
236
|
+
end
|
|
237
|
+
end
|
|
238
|
+
end
|
|
239
|
+
|
|
240
|
+
describe "Bio::Ucsc::Rn4::ChainAilMel1Link" do
|
|
241
|
+
context ".first" do
|
|
242
|
+
it 'returns the first records' do
|
|
243
|
+
result = Bio::Ucsc::Rn4::ChainAilMel1Link.first
|
|
244
|
+
pp result
|
|
245
|
+
result.should be_true
|
|
246
|
+
end
|
|
247
|
+
end
|
|
248
|
+
end
|
|
249
|
+
|
|
250
|
+
describe "Bio::Ucsc::Rn4::ChainBosTau3" do
|
|
251
|
+
context ".find_by_interval" do
|
|
252
|
+
it 'returns the first records' do
|
|
253
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
254
|
+
result = Bio::Ucsc::Rn4::ChainBosTau3.find_by_interval gi
|
|
255
|
+
pp result
|
|
256
|
+
result.should be_true
|
|
257
|
+
end
|
|
258
|
+
end
|
|
259
|
+
end
|
|
260
|
+
|
|
261
|
+
describe "Bio::Ucsc::Rn4::ChainBosTau3Link" do
|
|
262
|
+
context ".find_by_interval" do
|
|
263
|
+
it 'returns the first records' do
|
|
264
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
265
|
+
result = Bio::Ucsc::Rn4::ChainBosTau3Link.find_by_interval gi
|
|
266
|
+
pp result
|
|
267
|
+
result.should be_true
|
|
268
|
+
end
|
|
269
|
+
end
|
|
270
|
+
end
|
|
271
|
+
|
|
272
|
+
describe "Bio::Ucsc::Rn4::ChainCanFam2" do
|
|
273
|
+
context ".find_by_interval" do
|
|
274
|
+
it 'returns the first records' do
|
|
275
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
276
|
+
result = Bio::Ucsc::Rn4::ChainCanFam2.find_by_interval gi
|
|
277
|
+
pp result
|
|
278
|
+
result.should be_true
|
|
279
|
+
end
|
|
280
|
+
end
|
|
281
|
+
end
|
|
282
|
+
|
|
283
|
+
describe "Bio::Ucsc::Rn4::ChainCanFam2Link" do
|
|
284
|
+
context ".find_by_interval" do
|
|
285
|
+
it 'returns the first records' do
|
|
286
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
287
|
+
result = Bio::Ucsc::Rn4::ChainCanFam2Link.find_by_interval gi
|
|
288
|
+
pp result
|
|
289
|
+
result.should be_true
|
|
290
|
+
end
|
|
291
|
+
end
|
|
292
|
+
end
|
|
293
|
+
|
|
294
|
+
describe "Bio::Ucsc::Rn4::ChainCavPor3" do
|
|
295
|
+
context ".find_by_interval" do
|
|
296
|
+
it 'returns the first records' do
|
|
297
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
298
|
+
result = Bio::Ucsc::Rn4::ChainCavPor3.find_by_interval gi
|
|
299
|
+
pp result
|
|
300
|
+
result.should be_true
|
|
301
|
+
end
|
|
302
|
+
end
|
|
303
|
+
end
|
|
304
|
+
|
|
305
|
+
describe "Bio::Ucsc::Rn4::ChainCavPor3Link" do
|
|
306
|
+
context ".find_by_interval" do
|
|
307
|
+
it 'returns the first records' do
|
|
308
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
309
|
+
result = Bio::Ucsc::Rn4::ChainCavPor3Link.find_by_interval gi
|
|
310
|
+
pp result
|
|
311
|
+
result.should be_true
|
|
312
|
+
end
|
|
313
|
+
end
|
|
314
|
+
end
|
|
315
|
+
|
|
316
|
+
describe "Bio::Ucsc::Rn4::ChainDanRer4" do
|
|
317
|
+
context ".find_by_interval" do
|
|
318
|
+
it 'returns the first records' do
|
|
319
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
320
|
+
result = Bio::Ucsc::Rn4::ChainDanRer4.find_by_interval gi
|
|
321
|
+
pp result
|
|
322
|
+
result.should be_true
|
|
323
|
+
end
|
|
324
|
+
end
|
|
325
|
+
end
|
|
326
|
+
|
|
327
|
+
describe "Bio::Ucsc::Rn4::ChainDanRer4Link" do
|
|
328
|
+
context ".find_by_interval" do
|
|
329
|
+
it 'returns the first records' do
|
|
330
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
331
|
+
result = Bio::Ucsc::Rn4::ChainDanRer4Link.find_by_interval gi
|
|
332
|
+
pp result
|
|
333
|
+
result.should be_true
|
|
334
|
+
end
|
|
335
|
+
end
|
|
336
|
+
end
|
|
337
|
+
|
|
338
|
+
describe "Bio::Ucsc::Rn4::ChainEquCab1" do
|
|
339
|
+
context ".find_by_interval" do
|
|
340
|
+
it 'returns the first records' do
|
|
341
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
342
|
+
result = Bio::Ucsc::Rn4::ChainEquCab1.find_by_interval gi
|
|
343
|
+
pp result
|
|
344
|
+
result.should be_true
|
|
345
|
+
end
|
|
346
|
+
end
|
|
347
|
+
end
|
|
348
|
+
|
|
349
|
+
describe "Bio::Ucsc::Rn4::ChainEquCab1Link" do
|
|
350
|
+
context ".find_by_interval" do
|
|
351
|
+
it 'returns the first records' do
|
|
352
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
353
|
+
result = Bio::Ucsc::Rn4::ChainEquCab1Link.find_by_interval gi
|
|
354
|
+
pp result
|
|
355
|
+
result.should be_true
|
|
356
|
+
end
|
|
357
|
+
end
|
|
358
|
+
end
|
|
359
|
+
|
|
360
|
+
describe "Bio::Ucsc::Rn4::ChainGalGal3" do
|
|
361
|
+
context ".find_by_interval" do
|
|
362
|
+
it 'returns the first records' do
|
|
363
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
364
|
+
result = Bio::Ucsc::Rn4::ChainGalGal3.find_by_interval gi
|
|
365
|
+
pp result
|
|
366
|
+
result.should be_true
|
|
367
|
+
end
|
|
368
|
+
end
|
|
369
|
+
end
|
|
370
|
+
|
|
371
|
+
describe "Bio::Ucsc::Rn4::ChainGalGal3Link" do
|
|
372
|
+
context ".find_by_interval" do
|
|
373
|
+
it 'returns the first records' do
|
|
374
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
375
|
+
result = Bio::Ucsc::Rn4::ChainGalGal3Link.find_by_interval gi
|
|
376
|
+
pp result
|
|
377
|
+
result.should be_true
|
|
378
|
+
end
|
|
379
|
+
end
|
|
380
|
+
end
|
|
381
|
+
|
|
382
|
+
describe "Bio::Ucsc::Rn4::ChainHg19" do
|
|
383
|
+
context ".first" do
|
|
384
|
+
it 'returns the first records' do
|
|
385
|
+
result = Bio::Ucsc::Rn4::ChainHg19.first
|
|
386
|
+
pp result
|
|
387
|
+
result.should be_true
|
|
388
|
+
end
|
|
389
|
+
end
|
|
390
|
+
end
|
|
391
|
+
|
|
392
|
+
describe "Bio::Ucsc::Rn4::ChainHg19Link" do
|
|
393
|
+
context ".first" do
|
|
394
|
+
it 'returns the first records' do
|
|
395
|
+
result = Bio::Ucsc::Rn4::ChainHg19Link.first
|
|
396
|
+
pp result
|
|
397
|
+
result.should be_true
|
|
398
|
+
end
|
|
399
|
+
end
|
|
400
|
+
end
|
|
401
|
+
|
|
402
|
+
describe "Bio::Ucsc::Rn4::ChainMm9" do
|
|
403
|
+
context ".find_by_interval" do
|
|
404
|
+
it 'returns the first records' do
|
|
405
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
406
|
+
result = Bio::Ucsc::Rn4::ChainMm9.find_by_interval gi
|
|
407
|
+
pp result
|
|
408
|
+
result.should be_true
|
|
409
|
+
end
|
|
410
|
+
end
|
|
411
|
+
end
|
|
412
|
+
|
|
413
|
+
describe "Bio::Ucsc::Rn4::ChainMm9Link" do
|
|
414
|
+
context ".find_by_interval" do
|
|
415
|
+
it 'returns the first records' do
|
|
416
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
417
|
+
result = Bio::Ucsc::Rn4::ChainMm9Link.find_by_interval gi
|
|
418
|
+
pp result
|
|
419
|
+
result.should be_true
|
|
420
|
+
end
|
|
421
|
+
end
|
|
422
|
+
end
|
|
423
|
+
|
|
424
|
+
describe "Bio::Ucsc::Rn4::ChainMonDom4" do
|
|
425
|
+
context ".find_by_interval" do
|
|
426
|
+
it 'returns the first records' do
|
|
427
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
428
|
+
result = Bio::Ucsc::Rn4::ChainMonDom4.find_by_interval gi
|
|
429
|
+
pp result
|
|
430
|
+
result.should be_true
|
|
431
|
+
end
|
|
432
|
+
end
|
|
433
|
+
end
|
|
434
|
+
|
|
435
|
+
describe "Bio::Ucsc::Rn4::ChainMonDom4Link" do
|
|
436
|
+
context ".find_by_interval" do
|
|
437
|
+
it 'returns the first records' do
|
|
438
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
439
|
+
result = Bio::Ucsc::Rn4::ChainMonDom4Link.find_by_interval gi
|
|
440
|
+
pp result
|
|
441
|
+
result.should be_true
|
|
442
|
+
end
|
|
443
|
+
end
|
|
444
|
+
end
|
|
445
|
+
|
|
446
|
+
describe "Bio::Ucsc::Rn4::ChainPanTro2" do
|
|
447
|
+
context ".find_by_interval" do
|
|
448
|
+
it 'returns the first records' do
|
|
449
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
450
|
+
result = Bio::Ucsc::Rn4::ChainPanTro2.find_by_interval gi
|
|
451
|
+
pp result
|
|
452
|
+
result.should be_true
|
|
453
|
+
end
|
|
454
|
+
end
|
|
455
|
+
end
|
|
456
|
+
|
|
457
|
+
describe "Bio::Ucsc::Rn4::ChainPanTro2Link" do
|
|
458
|
+
context ".find_by_interval" do
|
|
459
|
+
it 'returns the first records' do
|
|
460
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
461
|
+
result = Bio::Ucsc::Rn4::ChainPanTro2Link.find_by_interval gi
|
|
462
|
+
pp result
|
|
463
|
+
result.should be_true
|
|
464
|
+
end
|
|
465
|
+
end
|
|
466
|
+
end
|
|
467
|
+
|
|
468
|
+
describe "Bio::Ucsc::Rn4::ChainRheMac2" do
|
|
469
|
+
context ".find_by_interval" do
|
|
470
|
+
it 'returns the first records' do
|
|
471
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
472
|
+
result = Bio::Ucsc::Rn4::ChainRheMac2.find_by_interval gi
|
|
473
|
+
pp result
|
|
474
|
+
result.should be_true
|
|
475
|
+
end
|
|
476
|
+
end
|
|
477
|
+
end
|
|
478
|
+
|
|
479
|
+
describe "Bio::Ucsc::Rn4::ChainRheMac2Link" do
|
|
480
|
+
context ".find_by_interval" do
|
|
481
|
+
it 'returns the first records' do
|
|
482
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
483
|
+
result = Bio::Ucsc::Rn4::ChainRheMac2Link.find_by_interval gi
|
|
484
|
+
pp result
|
|
485
|
+
result.should be_true
|
|
486
|
+
end
|
|
487
|
+
end
|
|
488
|
+
end
|
|
489
|
+
|
|
490
|
+
describe "Bio::Ucsc::Rn4::ChainXenTro2" do
|
|
491
|
+
context ".find_by_interval" do
|
|
492
|
+
it 'returns the first records' do
|
|
493
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
494
|
+
result = Bio::Ucsc::Rn4::ChainXenTro2.find_by_interval gi
|
|
495
|
+
pp result
|
|
496
|
+
result.should be_true
|
|
497
|
+
end
|
|
498
|
+
end
|
|
499
|
+
end
|
|
500
|
+
|
|
501
|
+
describe "Bio::Ucsc::Rn4::ChainXenTro2Link" do
|
|
502
|
+
context ".find_by_interval" do
|
|
503
|
+
it 'returns the first records' do
|
|
504
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
505
|
+
result = Bio::Ucsc::Rn4::ChainXenTro2Link.find_by_interval gi
|
|
506
|
+
pp result
|
|
507
|
+
result.should be_true
|
|
508
|
+
end
|
|
509
|
+
end
|
|
510
|
+
end
|
|
511
|
+
|
|
512
|
+
describe "Bio::Ucsc::Rn4::ChromInfo" do
|
|
513
|
+
context ".first" do
|
|
514
|
+
it 'returns the first records' do
|
|
515
|
+
result = Bio::Ucsc::Rn4::ChromInfo.first
|
|
516
|
+
pp result
|
|
517
|
+
result.should be_true
|
|
518
|
+
end
|
|
519
|
+
end
|
|
520
|
+
end
|
|
521
|
+
|
|
522
|
+
describe "Bio::Ucsc::Rn4::ContrastGene" do
|
|
523
|
+
context ".first" do
|
|
524
|
+
it 'returns the first records' do
|
|
525
|
+
result = Bio::Ucsc::Rn4::ContrastGene.first
|
|
526
|
+
pp result
|
|
527
|
+
result.should be_true
|
|
528
|
+
end
|
|
529
|
+
end
|
|
530
|
+
end
|
|
531
|
+
|
|
532
|
+
describe "Bio::Ucsc::Rn4::CpgIslandExt" do
|
|
533
|
+
context ".first" do
|
|
534
|
+
it 'returns the first records' do
|
|
535
|
+
result = Bio::Ucsc::Rn4::CpgIslandExt.first
|
|
536
|
+
pp result
|
|
537
|
+
result.should be_true
|
|
538
|
+
end
|
|
539
|
+
end
|
|
540
|
+
end
|
|
541
|
+
|
|
542
|
+
describe "Bio::Ucsc::Rn4::CpgIslandGgfAndyMasked" do
|
|
543
|
+
context ".first" do
|
|
544
|
+
it 'returns the first records' do
|
|
545
|
+
result = Bio::Ucsc::Rn4::CpgIslandGgfAndyMasked.first
|
|
546
|
+
pp result
|
|
547
|
+
result.should be_true
|
|
548
|
+
end
|
|
549
|
+
end
|
|
550
|
+
end
|
|
551
|
+
|
|
552
|
+
describe "Bio::Ucsc::Rn4::CytoBand" do
|
|
553
|
+
context ".first" do
|
|
554
|
+
it 'returns the first records' do
|
|
555
|
+
result = Bio::Ucsc::Rn4::CytoBand.first
|
|
556
|
+
pp result
|
|
557
|
+
result.should be_true
|
|
558
|
+
end
|
|
559
|
+
end
|
|
560
|
+
end
|
|
561
|
+
|
|
562
|
+
describe "Bio::Ucsc::Rn4::CytoBandIdeo" do
|
|
563
|
+
context ".first" do
|
|
564
|
+
it 'returns the first records' do
|
|
565
|
+
result = Bio::Ucsc::Rn4::CytoBandIdeo.first
|
|
566
|
+
pp result
|
|
567
|
+
result.should be_true
|
|
568
|
+
end
|
|
569
|
+
end
|
|
570
|
+
end
|
|
571
|
+
|
|
572
|
+
describe "Bio::Ucsc::Rn4::Description" do
|
|
573
|
+
context ".first" do
|
|
574
|
+
it 'returns the first records' do
|
|
575
|
+
result = Bio::Ucsc::Rn4::Description.first
|
|
576
|
+
pp result
|
|
577
|
+
result.should be_true
|
|
578
|
+
end
|
|
579
|
+
end
|
|
580
|
+
end
|
|
581
|
+
|
|
582
|
+
describe "Bio::Ucsc::Rn4::Development" do
|
|
583
|
+
context ".first" do
|
|
584
|
+
it 'returns the first records' do
|
|
585
|
+
result = Bio::Ucsc::Rn4::Development.first
|
|
586
|
+
pp result
|
|
587
|
+
result.should be_true
|
|
588
|
+
end
|
|
589
|
+
end
|
|
590
|
+
end
|
|
591
|
+
|
|
592
|
+
describe "Bio::Ucsc::Rn4::DmBlastTab" do
|
|
593
|
+
context ".first" do
|
|
594
|
+
it 'returns the first records' do
|
|
595
|
+
result = Bio::Ucsc::Rn4::DmBlastTab.first
|
|
596
|
+
pp result
|
|
597
|
+
result.should be_true
|
|
598
|
+
end
|
|
599
|
+
end
|
|
600
|
+
end
|
|
601
|
+
|
|
602
|
+
describe "Bio::Ucsc::Rn4::DrBlastTab" do
|
|
603
|
+
context ".first" do
|
|
604
|
+
it 'returns the first records' do
|
|
605
|
+
result = Bio::Ucsc::Rn4::DrBlastTab.first
|
|
606
|
+
pp result
|
|
607
|
+
result.should be_true
|
|
608
|
+
end
|
|
609
|
+
end
|
|
610
|
+
end
|
|
611
|
+
|
|
612
|
+
describe "Bio::Ucsc::Rn4::DupSpMrna" do
|
|
613
|
+
context ".first" do
|
|
614
|
+
it 'returns the first records' do
|
|
615
|
+
result = Bio::Ucsc::Rn4::DupSpMrna.first
|
|
616
|
+
pp result
|
|
617
|
+
result.should be_true
|
|
618
|
+
end
|
|
619
|
+
end
|
|
620
|
+
end
|
|
621
|
+
|
|
622
|
+
describe "Bio::Ucsc::Rn4::EnsGene" do
|
|
623
|
+
context ".first" do
|
|
624
|
+
it 'returns the first records' do
|
|
625
|
+
result = Bio::Ucsc::Rn4::EnsGene.first
|
|
626
|
+
pp result
|
|
627
|
+
result.should be_true
|
|
628
|
+
end
|
|
629
|
+
end
|
|
630
|
+
end
|
|
631
|
+
|
|
632
|
+
describe "Bio::Ucsc::Rn4::EnsGtp" do
|
|
633
|
+
context ".first" do
|
|
634
|
+
it 'returns the first records' do
|
|
635
|
+
result = Bio::Ucsc::Rn4::EnsGtp.first
|
|
636
|
+
pp result
|
|
637
|
+
result.should be_true
|
|
638
|
+
end
|
|
639
|
+
end
|
|
640
|
+
end
|
|
641
|
+
|
|
642
|
+
describe "Bio::Ucsc::Rn4::EnsPep" do
|
|
643
|
+
context ".first" do
|
|
644
|
+
it 'returns the first records' do
|
|
645
|
+
result = Bio::Ucsc::Rn4::EnsPep.first
|
|
646
|
+
pp result
|
|
647
|
+
result.should be_true
|
|
648
|
+
end
|
|
649
|
+
end
|
|
650
|
+
end
|
|
651
|
+
|
|
652
|
+
describe "Bio::Ucsc::Rn4::EnsemblXref3" do
|
|
653
|
+
context ".first" do
|
|
654
|
+
it 'returns the first records' do
|
|
655
|
+
result = Bio::Ucsc::Rn4::EnsemblXref3.first
|
|
656
|
+
pp result
|
|
657
|
+
result.should be_true
|
|
658
|
+
end
|
|
659
|
+
end
|
|
660
|
+
end
|
|
661
|
+
|
|
662
|
+
describe "Bio::Ucsc::Rn4::Est" do
|
|
663
|
+
context ".find_by_interval" do
|
|
664
|
+
it 'returns the first records' do
|
|
665
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
666
|
+
result = Bio::Ucsc::Rn4::Est.find_by_interval gi
|
|
667
|
+
pp result
|
|
668
|
+
result.should be_true
|
|
669
|
+
end
|
|
670
|
+
end
|
|
671
|
+
end
|
|
672
|
+
|
|
673
|
+
describe "Bio::Ucsc::Rn4::EstOrientInfo" do
|
|
674
|
+
context ".first" do
|
|
675
|
+
it 'returns the first records' do
|
|
676
|
+
result = Bio::Ucsc::Rn4::EstOrientInfo.first
|
|
677
|
+
pp result
|
|
678
|
+
result.should be_true
|
|
679
|
+
end
|
|
680
|
+
end
|
|
681
|
+
end
|
|
682
|
+
|
|
683
|
+
describe "Bio::Ucsc::Rn4::ExtFile" do
|
|
684
|
+
context ".first" do
|
|
685
|
+
it 'returns the first records' do
|
|
686
|
+
result = Bio::Ucsc::Rn4::ExtFile.first
|
|
687
|
+
pp result
|
|
688
|
+
result.should be_true
|
|
689
|
+
end
|
|
690
|
+
end
|
|
691
|
+
end
|
|
692
|
+
|
|
693
|
+
describe "Bio::Ucsc::Rn4::Gap" do
|
|
694
|
+
context ".find_by_interval" do
|
|
695
|
+
it 'returns the first records' do
|
|
696
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
697
|
+
result = Bio::Ucsc::Rn4::Gap.find_by_interval gi
|
|
698
|
+
pp result
|
|
699
|
+
result.should be_true
|
|
700
|
+
end
|
|
701
|
+
end
|
|
702
|
+
end
|
|
703
|
+
|
|
704
|
+
describe "Bio::Ucsc::Rn4::GbCdnaInfo" do
|
|
705
|
+
context ".first" do
|
|
706
|
+
it 'returns the first records' do
|
|
707
|
+
result = Bio::Ucsc::Rn4::GbCdnaInfo.first
|
|
708
|
+
pp result
|
|
709
|
+
result.should be_true
|
|
710
|
+
end
|
|
711
|
+
end
|
|
712
|
+
end
|
|
713
|
+
|
|
714
|
+
describe "Bio::Ucsc::Rn4::GbExtFile" do
|
|
715
|
+
context ".first" do
|
|
716
|
+
it 'returns the first records' do
|
|
717
|
+
result = Bio::Ucsc::Rn4::GbExtFile.first
|
|
718
|
+
pp result
|
|
719
|
+
result.should be_true
|
|
720
|
+
end
|
|
721
|
+
end
|
|
722
|
+
end
|
|
723
|
+
|
|
724
|
+
describe "Bio::Ucsc::Rn4::GbLoaded" do
|
|
725
|
+
context ".first" do
|
|
726
|
+
it 'returns the first records' do
|
|
727
|
+
result = Bio::Ucsc::Rn4::GbLoaded.first
|
|
728
|
+
pp result
|
|
729
|
+
result.should be_true
|
|
730
|
+
end
|
|
731
|
+
end
|
|
732
|
+
end
|
|
733
|
+
|
|
734
|
+
describe "Bio::Ucsc::Rn4::GbMiscDiff" do
|
|
735
|
+
context ".first" do
|
|
736
|
+
it 'returns the first records' do
|
|
737
|
+
result = Bio::Ucsc::Rn4::GbMiscDiff.first
|
|
738
|
+
pp result
|
|
739
|
+
result.should be_true
|
|
740
|
+
end
|
|
741
|
+
end
|
|
742
|
+
end
|
|
743
|
+
|
|
744
|
+
describe "Bio::Ucsc::Rn4::GbSeq" do
|
|
745
|
+
context ".first" do
|
|
746
|
+
it 'returns the first records' do
|
|
747
|
+
result = Bio::Ucsc::Rn4::GbSeq.first
|
|
748
|
+
pp result
|
|
749
|
+
result.should be_true
|
|
750
|
+
end
|
|
751
|
+
end
|
|
752
|
+
end
|
|
753
|
+
|
|
754
|
+
describe "Bio::Ucsc::Rn4::GbStatus" do
|
|
755
|
+
context ".first" do
|
|
756
|
+
it 'returns the first records' do
|
|
757
|
+
result = Bio::Ucsc::Rn4::GbStatus.first
|
|
758
|
+
pp result
|
|
759
|
+
result.should be_true
|
|
760
|
+
end
|
|
761
|
+
end
|
|
762
|
+
end
|
|
763
|
+
|
|
764
|
+
describe "Bio::Ucsc::Rn4::GbWarn" do
|
|
765
|
+
context ".first" do
|
|
766
|
+
it 'returns the first records' do
|
|
767
|
+
result = Bio::Ucsc::Rn4::GbWarn.first
|
|
768
|
+
pp result
|
|
769
|
+
result.should be_true
|
|
770
|
+
end
|
|
771
|
+
end
|
|
772
|
+
end
|
|
773
|
+
|
|
774
|
+
describe "Bio::Ucsc::Rn4::Gc5Base" do
|
|
775
|
+
context ".first" do
|
|
776
|
+
it 'returns the first records' do
|
|
777
|
+
result = Bio::Ucsc::Rn4::Gc5Base.first
|
|
778
|
+
pp result
|
|
779
|
+
result.should be_true
|
|
780
|
+
end
|
|
781
|
+
end
|
|
782
|
+
end
|
|
783
|
+
|
|
784
|
+
describe "Bio::Ucsc::Rn4::GeneName" do
|
|
785
|
+
context ".first" do
|
|
786
|
+
it 'returns the first records' do
|
|
787
|
+
result = Bio::Ucsc::Rn4::GeneName.first
|
|
788
|
+
pp result
|
|
789
|
+
result.should be_true
|
|
790
|
+
end
|
|
791
|
+
end
|
|
792
|
+
end
|
|
793
|
+
|
|
794
|
+
describe "Bio::Ucsc::Rn4::GeneNetworkId" do
|
|
795
|
+
context ".first" do
|
|
796
|
+
it 'returns the first records' do
|
|
797
|
+
result = Bio::Ucsc::Rn4::GeneNetworkId.first
|
|
798
|
+
pp result
|
|
799
|
+
result.should be_true
|
|
800
|
+
end
|
|
801
|
+
end
|
|
802
|
+
end
|
|
803
|
+
|
|
804
|
+
describe "Bio::Ucsc::Rn4::Geneid" do
|
|
805
|
+
context ".first" do
|
|
806
|
+
it 'returns the first records' do
|
|
807
|
+
result = Bio::Ucsc::Rn4::Geneid.first
|
|
808
|
+
pp result
|
|
809
|
+
result.should be_true
|
|
810
|
+
end
|
|
811
|
+
end
|
|
812
|
+
end
|
|
813
|
+
|
|
814
|
+
describe "Bio::Ucsc::Rn4::GeneidPep" do
|
|
815
|
+
context ".first" do
|
|
816
|
+
it 'returns the first records' do
|
|
817
|
+
result = Bio::Ucsc::Rn4::GeneidPep.first
|
|
818
|
+
pp result
|
|
819
|
+
result.should be_true
|
|
820
|
+
end
|
|
821
|
+
end
|
|
822
|
+
end
|
|
823
|
+
|
|
824
|
+
describe "Bio::Ucsc::Rn4::Genscan" do
|
|
825
|
+
context ".first" do
|
|
826
|
+
it 'returns the first records' do
|
|
827
|
+
result = Bio::Ucsc::Rn4::Genscan.first
|
|
828
|
+
pp result
|
|
829
|
+
result.should be_true
|
|
830
|
+
end
|
|
831
|
+
end
|
|
832
|
+
end
|
|
833
|
+
|
|
834
|
+
describe "Bio::Ucsc::Rn4::GenscanPep" do
|
|
835
|
+
context ".first" do
|
|
836
|
+
it 'returns the first records' do
|
|
837
|
+
result = Bio::Ucsc::Rn4::GenscanPep.first
|
|
838
|
+
pp result
|
|
839
|
+
result.should be_true
|
|
840
|
+
end
|
|
841
|
+
end
|
|
842
|
+
end
|
|
843
|
+
|
|
844
|
+
describe "Bio::Ucsc::Rn4::GnfAtlas2" do
|
|
845
|
+
context ".first" do
|
|
846
|
+
it 'returns the first records' do
|
|
847
|
+
result = Bio::Ucsc::Rn4::GnfAtlas2.first
|
|
848
|
+
pp result
|
|
849
|
+
result.should be_true
|
|
850
|
+
end
|
|
851
|
+
end
|
|
852
|
+
end
|
|
853
|
+
|
|
854
|
+
describe "Bio::Ucsc::Rn4::GnfAtlas2Distance" do
|
|
855
|
+
context ".first" do
|
|
856
|
+
it 'returns the first records' do
|
|
857
|
+
result = Bio::Ucsc::Rn4::GnfAtlas2Distance.first
|
|
858
|
+
pp result
|
|
859
|
+
result.should be_true
|
|
860
|
+
end
|
|
861
|
+
end
|
|
862
|
+
end
|
|
863
|
+
|
|
864
|
+
describe "Bio::Ucsc::Rn4::Gold" do
|
|
865
|
+
context ".find_by_interval" do
|
|
866
|
+
it 'returns the first records' do
|
|
867
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
868
|
+
result = Bio::Ucsc::Rn4::Gold.find_by_interval gi
|
|
869
|
+
pp result
|
|
870
|
+
result.should be_true
|
|
871
|
+
end
|
|
872
|
+
end
|
|
873
|
+
end
|
|
874
|
+
|
|
875
|
+
describe "Bio::Ucsc::Rn4::Grp" do
|
|
876
|
+
context ".first" do
|
|
877
|
+
it 'returns the first records' do
|
|
878
|
+
result = Bio::Ucsc::Rn4::Grp.first
|
|
879
|
+
pp result
|
|
880
|
+
result.should be_true
|
|
881
|
+
end
|
|
882
|
+
end
|
|
883
|
+
end
|
|
884
|
+
|
|
885
|
+
describe "Bio::Ucsc::Rn4::HgBlastTab" do
|
|
886
|
+
context ".first" do
|
|
887
|
+
it 'returns the first records' do
|
|
888
|
+
result = Bio::Ucsc::Rn4::HgBlastTab.first
|
|
889
|
+
pp result
|
|
890
|
+
result.should be_true
|
|
891
|
+
end
|
|
892
|
+
end
|
|
893
|
+
end
|
|
894
|
+
|
|
895
|
+
describe "Bio::Ucsc::Rn4::HgFindSpec" do
|
|
896
|
+
context ".first" do
|
|
897
|
+
it 'returns the first records' do
|
|
898
|
+
result = Bio::Ucsc::Rn4::HgFindSpec.first
|
|
899
|
+
pp result
|
|
900
|
+
result.should be_true
|
|
901
|
+
end
|
|
902
|
+
end
|
|
903
|
+
end
|
|
904
|
+
|
|
905
|
+
describe "Bio::Ucsc::Rn4::History" do
|
|
906
|
+
context ".first" do
|
|
907
|
+
it 'returns the first records' do
|
|
908
|
+
result = Bio::Ucsc::Rn4::History.first
|
|
909
|
+
pp result
|
|
910
|
+
result.should be_true
|
|
911
|
+
end
|
|
912
|
+
end
|
|
913
|
+
end
|
|
914
|
+
|
|
915
|
+
describe "Bio::Ucsc::Rn4::ImageClone" do
|
|
916
|
+
context ".first" do
|
|
917
|
+
it 'returns the first records' do
|
|
918
|
+
result = Bio::Ucsc::Rn4::ImageClone.first
|
|
919
|
+
pp result
|
|
920
|
+
result.should be_true
|
|
921
|
+
end
|
|
922
|
+
end
|
|
923
|
+
end
|
|
924
|
+
|
|
925
|
+
describe "Bio::Ucsc::Rn4::IntronEst" do
|
|
926
|
+
context ".find_by_interval" do
|
|
927
|
+
it 'returns the first records' do
|
|
928
|
+
gi = Bio::GenomicInterval.parse("chrX:1-1,000,000")
|
|
929
|
+
result = Bio::Ucsc::Rn4::IntronEst.find_by_interval gi
|
|
930
|
+
pp result
|
|
931
|
+
result.should be_true
|
|
932
|
+
end
|
|
933
|
+
end
|
|
934
|
+
end
|
|
935
|
+
|
|
936
|
+
describe "Bio::Ucsc::Rn4::KeggMapDesc" do
|
|
937
|
+
context ".first" do
|
|
938
|
+
it 'returns the first records' do
|
|
939
|
+
result = Bio::Ucsc::Rn4::KeggMapDesc.first
|
|
940
|
+
pp result
|
|
941
|
+
result.should be_true
|
|
942
|
+
end
|
|
943
|
+
end
|
|
944
|
+
end
|
|
945
|
+
|
|
946
|
+
describe "Bio::Ucsc::Rn4::KeggPathway" do
|
|
947
|
+
context ".first" do
|
|
948
|
+
it 'returns the first records' do
|
|
949
|
+
result = Bio::Ucsc::Rn4::KeggPathway.first
|
|
950
|
+
pp result
|
|
951
|
+
result.should be_true
|
|
952
|
+
end
|
|
953
|
+
end
|
|
954
|
+
end
|
|
955
|
+
|
|
956
|
+
describe "Bio::Ucsc::Rn4::Keyword" do
|
|
957
|
+
context ".first" do
|
|
958
|
+
it 'returns the first records' do
|
|
959
|
+
result = Bio::Ucsc::Rn4::Keyword.first
|
|
960
|
+
pp result
|
|
961
|
+
result.should be_true
|
|
962
|
+
end
|
|
963
|
+
end
|
|
964
|
+
end
|
|
965
|
+
|
|
966
|
+
describe "Bio::Ucsc::Rn4::KgAlias" do
|
|
967
|
+
context ".first" do
|
|
968
|
+
it 'returns the first records' do
|
|
969
|
+
result = Bio::Ucsc::Rn4::KgAlias.first
|
|
970
|
+
pp result
|
|
971
|
+
result.should be_true
|
|
972
|
+
end
|
|
973
|
+
end
|
|
974
|
+
end
|
|
975
|
+
|
|
976
|
+
describe "Bio::Ucsc::Rn4::KgProtAlias" do
|
|
977
|
+
context ".first" do
|
|
978
|
+
it 'returns the first records' do
|
|
979
|
+
result = Bio::Ucsc::Rn4::KgProtAlias.first
|
|
980
|
+
pp result
|
|
981
|
+
result.should be_true
|
|
982
|
+
end
|
|
983
|
+
end
|
|
984
|
+
end
|
|
985
|
+
|
|
986
|
+
describe "Bio::Ucsc::Rn4::KgProtMap" do
|
|
987
|
+
context ".first" do
|
|
988
|
+
it 'returns the first records' do
|
|
989
|
+
result = Bio::Ucsc::Rn4::KgProtMap.first
|
|
990
|
+
pp result
|
|
991
|
+
result.should be_true
|
|
992
|
+
end
|
|
993
|
+
end
|
|
994
|
+
end
|
|
995
|
+
|
|
996
|
+
describe "Bio::Ucsc::Rn4::KgSpAlias" do
|
|
997
|
+
context ".first" do
|
|
998
|
+
it 'returns the first records' do
|
|
999
|
+
result = Bio::Ucsc::Rn4::KgSpAlias.first
|
|
1000
|
+
pp result
|
|
1001
|
+
result.should be_true
|
|
1002
|
+
end
|
|
1003
|
+
end
|
|
1004
|
+
end
|
|
1005
|
+
|
|
1006
|
+
describe "Bio::Ucsc::Rn4::KgXref" do
|
|
1007
|
+
context ".first" do
|
|
1008
|
+
it 'returns the first records' do
|
|
1009
|
+
result = Bio::Ucsc::Rn4::KgXref.first
|
|
1010
|
+
pp result
|
|
1011
|
+
result.should be_true
|
|
1012
|
+
end
|
|
1013
|
+
end
|
|
1014
|
+
end
|
|
1015
|
+
|
|
1016
|
+
describe "Bio::Ucsc::Rn4::KnownBlastTab" do
|
|
1017
|
+
context ".first" do
|
|
1018
|
+
it 'returns the first records' do
|
|
1019
|
+
result = Bio::Ucsc::Rn4::KnownBlastTab.first
|
|
1020
|
+
pp result
|
|
1021
|
+
result.should be_true
|
|
1022
|
+
end
|
|
1023
|
+
end
|
|
1024
|
+
end
|
|
1025
|
+
|
|
1026
|
+
describe "Bio::Ucsc::Rn4::KnownCanonical" do
|
|
1027
|
+
context ".first" do
|
|
1028
|
+
it 'returns the first records' do
|
|
1029
|
+
result = Bio::Ucsc::Rn4::KnownCanonical.first
|
|
1030
|
+
pp result
|
|
1031
|
+
result.should be_true
|
|
1032
|
+
end
|
|
1033
|
+
end
|
|
1034
|
+
end
|
|
1035
|
+
|
|
1036
|
+
describe "Bio::Ucsc::Rn4::KnownGene" do
|
|
1037
|
+
context ".first" do
|
|
1038
|
+
it 'returns the first records' do
|
|
1039
|
+
result = Bio::Ucsc::Rn4::KnownGene.first
|
|
1040
|
+
pp result
|
|
1041
|
+
result.should be_true
|
|
1042
|
+
end
|
|
1043
|
+
end
|
|
1044
|
+
end
|
|
1045
|
+
|
|
1046
|
+
describe "Bio::Ucsc::Rn4::KnownGeneMrna" do
|
|
1047
|
+
context ".first" do
|
|
1048
|
+
it 'returns the first records' do
|
|
1049
|
+
result = Bio::Ucsc::Rn4::KnownGeneMrna.first
|
|
1050
|
+
pp result
|
|
1051
|
+
result.should be_true
|
|
1052
|
+
end
|
|
1053
|
+
end
|
|
1054
|
+
end
|
|
1055
|
+
|
|
1056
|
+
describe "Bio::Ucsc::Rn4::KnownGenePep" do
|
|
1057
|
+
context ".first" do
|
|
1058
|
+
it 'returns the first records' do
|
|
1059
|
+
result = Bio::Ucsc::Rn4::KnownGenePep.first
|
|
1060
|
+
pp result
|
|
1061
|
+
result.should be_true
|
|
1062
|
+
end
|
|
1063
|
+
end
|
|
1064
|
+
end
|
|
1065
|
+
|
|
1066
|
+
describe "Bio::Ucsc::Rn4::KnownIsoforms" do
|
|
1067
|
+
context ".first" do
|
|
1068
|
+
it 'returns the first records' do
|
|
1069
|
+
result = Bio::Ucsc::Rn4::KnownIsoforms.first
|
|
1070
|
+
pp result
|
|
1071
|
+
result.should be_true
|
|
1072
|
+
end
|
|
1073
|
+
end
|
|
1074
|
+
end
|
|
1075
|
+
|
|
1076
|
+
describe "Bio::Ucsc::Rn4::KnownToEnsembl" do
|
|
1077
|
+
context ".first" do
|
|
1078
|
+
it 'returns the first records' do
|
|
1079
|
+
result = Bio::Ucsc::Rn4::KnownToEnsembl.first
|
|
1080
|
+
pp result
|
|
1081
|
+
result.should be_true
|
|
1082
|
+
end
|
|
1083
|
+
end
|
|
1084
|
+
end
|
|
1085
|
+
|
|
1086
|
+
describe "Bio::Ucsc::Rn4::KnownToGnfAtlas2" do
|
|
1087
|
+
context ".first" do
|
|
1088
|
+
it 'returns the first records' do
|
|
1089
|
+
result = Bio::Ucsc::Rn4::KnownToGnfAtlas2.first
|
|
1090
|
+
pp result
|
|
1091
|
+
result.should be_true
|
|
1092
|
+
end
|
|
1093
|
+
end
|
|
1094
|
+
end
|
|
1095
|
+
|
|
1096
|
+
describe "Bio::Ucsc::Rn4::KnownToKeggEntrez" do
|
|
1097
|
+
context ".first" do
|
|
1098
|
+
it 'returns the first records' do
|
|
1099
|
+
result = Bio::Ucsc::Rn4::KnownToKeggEntrez.first
|
|
1100
|
+
pp result
|
|
1101
|
+
result.should be_true
|
|
1102
|
+
end
|
|
1103
|
+
end
|
|
1104
|
+
end
|
|
1105
|
+
|
|
1106
|
+
describe "Bio::Ucsc::Rn4::KnownToLocusLink" do
|
|
1107
|
+
context ".first" do
|
|
1108
|
+
it 'returns the first records' do
|
|
1109
|
+
result = Bio::Ucsc::Rn4::KnownToLocusLink.first
|
|
1110
|
+
pp result
|
|
1111
|
+
result.should be_true
|
|
1112
|
+
end
|
|
1113
|
+
end
|
|
1114
|
+
end
|
|
1115
|
+
|
|
1116
|
+
describe "Bio::Ucsc::Rn4::KnownToPfam" do
|
|
1117
|
+
context ".first" do
|
|
1118
|
+
it 'returns the first records' do
|
|
1119
|
+
result = Bio::Ucsc::Rn4::KnownToPfam.first
|
|
1120
|
+
pp result
|
|
1121
|
+
result.should be_true
|
|
1122
|
+
end
|
|
1123
|
+
end
|
|
1124
|
+
end
|
|
1125
|
+
|
|
1126
|
+
describe "Bio::Ucsc::Rn4::KnownToRAE230" do
|
|
1127
|
+
context ".first" do
|
|
1128
|
+
it 'returns the first records' do
|
|
1129
|
+
result = Bio::Ucsc::Rn4::KnownToRAE230.first
|
|
1130
|
+
pp result
|
|
1131
|
+
result.should be_true
|
|
1132
|
+
end
|
|
1133
|
+
end
|
|
1134
|
+
end
|
|
1135
|
+
|
|
1136
|
+
describe "Bio::Ucsc::Rn4::KnownToRefSeq" do
|
|
1137
|
+
context ".first" do
|
|
1138
|
+
it 'returns the first records' do
|
|
1139
|
+
result = Bio::Ucsc::Rn4::KnownToRefSeq.first
|
|
1140
|
+
pp result
|
|
1141
|
+
result.should be_true
|
|
1142
|
+
end
|
|
1143
|
+
end
|
|
1144
|
+
end
|
|
1145
|
+
|
|
1146
|
+
describe "Bio::Ucsc::Rn4::KnownToSuper" do
|
|
1147
|
+
context ".first" do
|
|
1148
|
+
it 'returns the first records' do
|
|
1149
|
+
result = Bio::Ucsc::Rn4::KnownToSuper.first
|
|
1150
|
+
pp result
|
|
1151
|
+
result.should be_true
|
|
1152
|
+
end
|
|
1153
|
+
end
|
|
1154
|
+
end
|
|
1155
|
+
|
|
1156
|
+
describe "Bio::Ucsc::Rn4::KnownToU34A" do
|
|
1157
|
+
context ".first" do
|
|
1158
|
+
it 'returns the first records' do
|
|
1159
|
+
result = Bio::Ucsc::Rn4::KnownToU34A.first
|
|
1160
|
+
pp result
|
|
1161
|
+
result.should be_true
|
|
1162
|
+
end
|
|
1163
|
+
end
|
|
1164
|
+
end
|
|
1165
|
+
|
|
1166
|
+
describe "Bio::Ucsc::Rn4::Library" do
|
|
1167
|
+
context ".first" do
|
|
1168
|
+
it 'returns the first records' do
|
|
1169
|
+
result = Bio::Ucsc::Rn4::Library.first
|
|
1170
|
+
pp result
|
|
1171
|
+
result.should be_true
|
|
1172
|
+
end
|
|
1173
|
+
end
|
|
1174
|
+
end
|
|
1175
|
+
|
|
1176
|
+
describe "Bio::Ucsc::Rn4::MgcFullMrna" do
|
|
1177
|
+
context ".first" do
|
|
1178
|
+
it 'returns the first records' do
|
|
1179
|
+
result = Bio::Ucsc::Rn4::MgcFullMrna.first
|
|
1180
|
+
pp result
|
|
1181
|
+
result.should be_true
|
|
1182
|
+
end
|
|
1183
|
+
end
|
|
1184
|
+
end
|
|
1185
|
+
|
|
1186
|
+
describe "Bio::Ucsc::Rn4::MgcGenes" do
|
|
1187
|
+
context ".first" do
|
|
1188
|
+
it 'returns the first records' do
|
|
1189
|
+
result = Bio::Ucsc::Rn4::MgcGenes.first
|
|
1190
|
+
pp result
|
|
1191
|
+
result.should be_true
|
|
1192
|
+
end
|
|
1193
|
+
end
|
|
1194
|
+
end
|
|
1195
|
+
|
|
1196
|
+
describe "Bio::Ucsc::Rn4::MiRNA" do
|
|
1197
|
+
context ".first" do
|
|
1198
|
+
it 'returns the first records' do
|
|
1199
|
+
result = Bio::Ucsc::Rn4::MiRNA.first
|
|
1200
|
+
pp result
|
|
1201
|
+
result.should be_true
|
|
1202
|
+
end
|
|
1203
|
+
end
|
|
1204
|
+
end
|
|
1205
|
+
|
|
1206
|
+
describe "Bio::Ucsc::Rn4::Microsat" do
|
|
1207
|
+
context ".first" do
|
|
1208
|
+
it 'returns the first records' do
|
|
1209
|
+
result = Bio::Ucsc::Rn4::Microsat.first
|
|
1210
|
+
pp result
|
|
1211
|
+
result.should be_true
|
|
1212
|
+
end
|
|
1213
|
+
end
|
|
1214
|
+
end
|
|
1215
|
+
|
|
1216
|
+
describe "Bio::Ucsc::Rn4::MmBlastTab" do
|
|
1217
|
+
context ".first" do
|
|
1218
|
+
it 'returns the first records' do
|
|
1219
|
+
result = Bio::Ucsc::Rn4::MmBlastTab.first
|
|
1220
|
+
pp result
|
|
1221
|
+
result.should be_true
|
|
1222
|
+
end
|
|
1223
|
+
end
|
|
1224
|
+
end
|
|
1225
|
+
|
|
1226
|
+
describe "Bio::Ucsc::Rn4::Mrna" do
|
|
1227
|
+
context ".find_by_interval" do
|
|
1228
|
+
it 'returns the first records' do
|
|
1229
|
+
gi = Bio::GenomicInterval.parse("chrX:1-5,000,000")
|
|
1230
|
+
result = Bio::Ucsc::Rn4::Mrna.find_by_interval gi
|
|
1231
|
+
pp result
|
|
1232
|
+
result.should be_true
|
|
1233
|
+
end
|
|
1234
|
+
end
|
|
1235
|
+
end
|
|
1236
|
+
|
|
1237
|
+
describe "Bio::Ucsc::Rn4::MrnaClone" do
|
|
1238
|
+
context ".first" do
|
|
1239
|
+
it 'returns the first records' do
|
|
1240
|
+
result = Bio::Ucsc::Rn4::MrnaClone.first
|
|
1241
|
+
pp result
|
|
1242
|
+
result.should be_true
|
|
1243
|
+
end
|
|
1244
|
+
end
|
|
1245
|
+
end
|
|
1246
|
+
|
|
1247
|
+
describe "Bio::Ucsc::Rn4::MrnaOrientInfo" do
|
|
1248
|
+
context ".first" do
|
|
1249
|
+
it 'returns the first records' do
|
|
1250
|
+
result = Bio::Ucsc::Rn4::MrnaOrientInfo.first
|
|
1251
|
+
pp result
|
|
1252
|
+
result.should be_true
|
|
1253
|
+
end
|
|
1254
|
+
end
|
|
1255
|
+
end
|
|
1256
|
+
|
|
1257
|
+
describe "Bio::Ucsc::Rn4::MrnaRefseq" do
|
|
1258
|
+
context ".first" do
|
|
1259
|
+
it 'returns the first records' do
|
|
1260
|
+
result = Bio::Ucsc::Rn4::MrnaRefseq.first
|
|
1261
|
+
pp result
|
|
1262
|
+
result.should be_true
|
|
1263
|
+
end
|
|
1264
|
+
end
|
|
1265
|
+
end
|
|
1266
|
+
|
|
1267
|
+
describe "Bio::Ucsc::Rn4::Multiz9way" do
|
|
1268
|
+
context ".first" do
|
|
1269
|
+
it 'returns the first records' do
|
|
1270
|
+
result = Bio::Ucsc::Rn4::Multiz9way.first
|
|
1271
|
+
pp result
|
|
1272
|
+
result.should be_true
|
|
1273
|
+
end
|
|
1274
|
+
end
|
|
1275
|
+
end
|
|
1276
|
+
|
|
1277
|
+
describe "Bio::Ucsc::Rn4::Multiz9wayFrames" do
|
|
1278
|
+
context ".first" do
|
|
1279
|
+
it 'returns the first records' do
|
|
1280
|
+
result = Bio::Ucsc::Rn4::Multiz9wayFrames.first
|
|
1281
|
+
pp result
|
|
1282
|
+
result.should be_true
|
|
1283
|
+
end
|
|
1284
|
+
end
|
|
1285
|
+
end
|
|
1286
|
+
|
|
1287
|
+
describe "Bio::Ucsc::Rn4::Multiz9waySummary" do
|
|
1288
|
+
context ".first" do
|
|
1289
|
+
it 'returns the first records' do
|
|
1290
|
+
result = Bio::Ucsc::Rn4::Multiz9waySummary.first
|
|
1291
|
+
pp result
|
|
1292
|
+
result.should be_true
|
|
1293
|
+
end
|
|
1294
|
+
end
|
|
1295
|
+
end
|
|
1296
|
+
|
|
1297
|
+
describe "Bio::Ucsc::Rn4::NetAilMel1" do
|
|
1298
|
+
context ".first" do
|
|
1299
|
+
it 'returns the first records' do
|
|
1300
|
+
result = Bio::Ucsc::Rn4::NetAilMel1.first
|
|
1301
|
+
pp result
|
|
1302
|
+
result.should be_true
|
|
1303
|
+
end
|
|
1304
|
+
end
|
|
1305
|
+
end
|
|
1306
|
+
|
|
1307
|
+
describe "Bio::Ucsc::Rn4::NetBosTau3" do
|
|
1308
|
+
context ".first" do
|
|
1309
|
+
it 'returns the first records' do
|
|
1310
|
+
result = Bio::Ucsc::Rn4::NetBosTau3.first
|
|
1311
|
+
pp result
|
|
1312
|
+
result.should be_true
|
|
1313
|
+
end
|
|
1314
|
+
end
|
|
1315
|
+
end
|
|
1316
|
+
|
|
1317
|
+
describe "Bio::Ucsc::Rn4::NetCanFam2" do
|
|
1318
|
+
context ".first" do
|
|
1319
|
+
it 'returns the first records' do
|
|
1320
|
+
result = Bio::Ucsc::Rn4::NetCanFam2.first
|
|
1321
|
+
pp result
|
|
1322
|
+
result.should be_true
|
|
1323
|
+
end
|
|
1324
|
+
end
|
|
1325
|
+
end
|
|
1326
|
+
|
|
1327
|
+
describe "Bio::Ucsc::Rn4::NetCavPor3" do
|
|
1328
|
+
context ".first" do
|
|
1329
|
+
it 'returns the first records' do
|
|
1330
|
+
result = Bio::Ucsc::Rn4::NetCavPor3.first
|
|
1331
|
+
pp result
|
|
1332
|
+
result.should be_true
|
|
1333
|
+
end
|
|
1334
|
+
end
|
|
1335
|
+
end
|
|
1336
|
+
|
|
1337
|
+
describe "Bio::Ucsc::Rn4::NetDanRer4" do
|
|
1338
|
+
context ".first" do
|
|
1339
|
+
it 'returns the first records' do
|
|
1340
|
+
result = Bio::Ucsc::Rn4::NetDanRer4.first
|
|
1341
|
+
pp result
|
|
1342
|
+
result.should be_true
|
|
1343
|
+
end
|
|
1344
|
+
end
|
|
1345
|
+
end
|
|
1346
|
+
|
|
1347
|
+
describe "Bio::Ucsc::Rn4::NetEquCab1" do
|
|
1348
|
+
context ".first" do
|
|
1349
|
+
it 'returns the first records' do
|
|
1350
|
+
result = Bio::Ucsc::Rn4::NetEquCab1.first
|
|
1351
|
+
pp result
|
|
1352
|
+
result.should be_true
|
|
1353
|
+
end
|
|
1354
|
+
end
|
|
1355
|
+
end
|
|
1356
|
+
|
|
1357
|
+
describe "Bio::Ucsc::Rn4::NetGalGal3" do
|
|
1358
|
+
context ".first" do
|
|
1359
|
+
it 'returns the first records' do
|
|
1360
|
+
result = Bio::Ucsc::Rn4::NetGalGal3.first
|
|
1361
|
+
pp result
|
|
1362
|
+
result.should be_true
|
|
1363
|
+
end
|
|
1364
|
+
end
|
|
1365
|
+
end
|
|
1366
|
+
|
|
1367
|
+
describe "Bio::Ucsc::Rn4::NetHg19" do
|
|
1368
|
+
context ".first" do
|
|
1369
|
+
it 'returns the first records' do
|
|
1370
|
+
result = Bio::Ucsc::Rn4::NetHg19.first
|
|
1371
|
+
pp result
|
|
1372
|
+
result.should be_true
|
|
1373
|
+
end
|
|
1374
|
+
end
|
|
1375
|
+
end
|
|
1376
|
+
|
|
1377
|
+
describe "Bio::Ucsc::Rn4::NetMm9" do
|
|
1378
|
+
context ".first" do
|
|
1379
|
+
it 'returns the first records' do
|
|
1380
|
+
result = Bio::Ucsc::Rn4::NetMm9.first
|
|
1381
|
+
pp result
|
|
1382
|
+
result.should be_true
|
|
1383
|
+
end
|
|
1384
|
+
end
|
|
1385
|
+
end
|
|
1386
|
+
|
|
1387
|
+
describe "Bio::Ucsc::Rn4::NetMonDom4" do
|
|
1388
|
+
context ".first" do
|
|
1389
|
+
it 'returns the first records' do
|
|
1390
|
+
result = Bio::Ucsc::Rn4::NetMonDom4.first
|
|
1391
|
+
pp result
|
|
1392
|
+
result.should be_true
|
|
1393
|
+
end
|
|
1394
|
+
end
|
|
1395
|
+
end
|
|
1396
|
+
|
|
1397
|
+
describe "Bio::Ucsc::Rn4::NetPanTro2" do
|
|
1398
|
+
context ".first" do
|
|
1399
|
+
it 'returns the first records' do
|
|
1400
|
+
result = Bio::Ucsc::Rn4::NetPanTro2.first
|
|
1401
|
+
pp result
|
|
1402
|
+
result.should be_true
|
|
1403
|
+
end
|
|
1404
|
+
end
|
|
1405
|
+
end
|
|
1406
|
+
|
|
1407
|
+
describe "Bio::Ucsc::Rn4::NetRheMac2" do
|
|
1408
|
+
context ".first" do
|
|
1409
|
+
it 'returns the first records' do
|
|
1410
|
+
result = Bio::Ucsc::Rn4::NetRheMac2.first
|
|
1411
|
+
pp result
|
|
1412
|
+
result.should be_true
|
|
1413
|
+
end
|
|
1414
|
+
end
|
|
1415
|
+
end
|
|
1416
|
+
|
|
1417
|
+
describe "Bio::Ucsc::Rn4::NetXenTro2" do
|
|
1418
|
+
context ".first" do
|
|
1419
|
+
it 'returns the first records' do
|
|
1420
|
+
result = Bio::Ucsc::Rn4::NetXenTro2.first
|
|
1421
|
+
pp result
|
|
1422
|
+
result.should be_true
|
|
1423
|
+
end
|
|
1424
|
+
end
|
|
1425
|
+
end
|
|
1426
|
+
|
|
1427
|
+
describe "Bio::Ucsc::Rn4::NscanGene" do
|
|
1428
|
+
context ".first" do
|
|
1429
|
+
it 'returns the first records' do
|
|
1430
|
+
result = Bio::Ucsc::Rn4::NscanGene.first
|
|
1431
|
+
pp result
|
|
1432
|
+
result.should be_true
|
|
1433
|
+
end
|
|
1434
|
+
end
|
|
1435
|
+
end
|
|
1436
|
+
|
|
1437
|
+
describe "Bio::Ucsc::Rn4::NscanPep" do
|
|
1438
|
+
context ".first" do
|
|
1439
|
+
it 'returns the first records' do
|
|
1440
|
+
result = Bio::Ucsc::Rn4::NscanPep.first
|
|
1441
|
+
pp result
|
|
1442
|
+
result.should be_true
|
|
1443
|
+
end
|
|
1444
|
+
end
|
|
1445
|
+
end
|
|
1446
|
+
|
|
1447
|
+
describe "Bio::Ucsc::Rn4::Organism" do
|
|
1448
|
+
context ".first" do
|
|
1449
|
+
it 'returns the first records' do
|
|
1450
|
+
result = Bio::Ucsc::Rn4::Organism.first
|
|
1451
|
+
pp result
|
|
1452
|
+
result.should be_true
|
|
1453
|
+
end
|
|
1454
|
+
end
|
|
1455
|
+
end
|
|
1456
|
+
|
|
1457
|
+
describe "Bio::Ucsc::Rn4::PbAnomLimit" do
|
|
1458
|
+
context ".first" do
|
|
1459
|
+
it 'returns the first records' do
|
|
1460
|
+
result = Bio::Ucsc::Rn4::PbAnomLimit.first
|
|
1461
|
+
pp result
|
|
1462
|
+
result.should be_true
|
|
1463
|
+
end
|
|
1464
|
+
end
|
|
1465
|
+
end
|
|
1466
|
+
|
|
1467
|
+
describe "Bio::Ucsc::Rn4::PbResAvgStd" do
|
|
1468
|
+
context ".first" do
|
|
1469
|
+
it 'returns the first records' do
|
|
1470
|
+
result = Bio::Ucsc::Rn4::PbResAvgStd.first
|
|
1471
|
+
pp result
|
|
1472
|
+
result.should be_true
|
|
1473
|
+
end
|
|
1474
|
+
end
|
|
1475
|
+
end
|
|
1476
|
+
|
|
1477
|
+
describe "Bio::Ucsc::Rn4::PbStamp" do
|
|
1478
|
+
context ".first" do
|
|
1479
|
+
it 'returns the first records' do
|
|
1480
|
+
result = Bio::Ucsc::Rn4::PbStamp.first
|
|
1481
|
+
pp result
|
|
1482
|
+
result.should be_true
|
|
1483
|
+
end
|
|
1484
|
+
end
|
|
1485
|
+
end
|
|
1486
|
+
|
|
1487
|
+
describe "Bio::Ucsc::Rn4::PepCCntDist" do
|
|
1488
|
+
context ".first" do
|
|
1489
|
+
it 'returns the first records' do
|
|
1490
|
+
result = Bio::Ucsc::Rn4::PepCCntDist.first
|
|
1491
|
+
pp result
|
|
1492
|
+
result.should be_true
|
|
1493
|
+
end
|
|
1494
|
+
end
|
|
1495
|
+
end
|
|
1496
|
+
|
|
1497
|
+
describe "Bio::Ucsc::Rn4::PepExonCntDist" do
|
|
1498
|
+
context ".first" do
|
|
1499
|
+
it 'returns the first records' do
|
|
1500
|
+
result = Bio::Ucsc::Rn4::PepExonCntDist.first
|
|
1501
|
+
pp result
|
|
1502
|
+
result.should be_true
|
|
1503
|
+
end
|
|
1504
|
+
end
|
|
1505
|
+
end
|
|
1506
|
+
|
|
1507
|
+
describe "Bio::Ucsc::Rn4::PepHydroDist" do
|
|
1508
|
+
context ".first" do
|
|
1509
|
+
it 'returns the first records' do
|
|
1510
|
+
result = Bio::Ucsc::Rn4::PepHydroDist.first
|
|
1511
|
+
pp result
|
|
1512
|
+
result.should be_true
|
|
1513
|
+
end
|
|
1514
|
+
end
|
|
1515
|
+
end
|
|
1516
|
+
|
|
1517
|
+
describe "Bio::Ucsc::Rn4::PepIPCntDist" do
|
|
1518
|
+
context ".first" do
|
|
1519
|
+
it 'returns the first records' do
|
|
1520
|
+
result = Bio::Ucsc::Rn4::PepIPCntDist.first
|
|
1521
|
+
pp result
|
|
1522
|
+
result.should be_true
|
|
1523
|
+
end
|
|
1524
|
+
end
|
|
1525
|
+
end
|
|
1526
|
+
|
|
1527
|
+
describe "Bio::Ucsc::Rn4::PepMolWtDist" do
|
|
1528
|
+
context ".first" do
|
|
1529
|
+
it 'returns the first records' do
|
|
1530
|
+
result = Bio::Ucsc::Rn4::PepMolWtDist.first
|
|
1531
|
+
pp result
|
|
1532
|
+
result.should be_true
|
|
1533
|
+
end
|
|
1534
|
+
end
|
|
1535
|
+
end
|
|
1536
|
+
|
|
1537
|
+
describe "Bio::Ucsc::Rn4::PepMwAa" do
|
|
1538
|
+
context ".first" do
|
|
1539
|
+
it 'returns the first records' do
|
|
1540
|
+
result = Bio::Ucsc::Rn4::PepMwAa.first
|
|
1541
|
+
pp result
|
|
1542
|
+
result.should be_true
|
|
1543
|
+
end
|
|
1544
|
+
end
|
|
1545
|
+
end
|
|
1546
|
+
|
|
1547
|
+
describe "Bio::Ucsc::Rn4::PepPi" do
|
|
1548
|
+
context ".first" do
|
|
1549
|
+
it 'returns the first records' do
|
|
1550
|
+
result = Bio::Ucsc::Rn4::PepPi.first
|
|
1551
|
+
pp result
|
|
1552
|
+
result.should be_true
|
|
1553
|
+
end
|
|
1554
|
+
end
|
|
1555
|
+
end
|
|
1556
|
+
|
|
1557
|
+
describe "Bio::Ucsc::Rn4::PepPiDist" do
|
|
1558
|
+
context ".first" do
|
|
1559
|
+
it 'returns the first records' do
|
|
1560
|
+
result = Bio::Ucsc::Rn4::PepPiDist.first
|
|
1561
|
+
pp result
|
|
1562
|
+
result.should be_true
|
|
1563
|
+
end
|
|
1564
|
+
end
|
|
1565
|
+
end
|
|
1566
|
+
|
|
1567
|
+
describe "Bio::Ucsc::Rn4::PepResDist" do
|
|
1568
|
+
context ".first" do
|
|
1569
|
+
it 'returns the first records' do
|
|
1570
|
+
result = Bio::Ucsc::Rn4::PepResDist.first
|
|
1571
|
+
pp result
|
|
1572
|
+
result.should be_true
|
|
1573
|
+
end
|
|
1574
|
+
end
|
|
1575
|
+
end
|
|
1576
|
+
|
|
1577
|
+
describe "Bio::Ucsc::Rn4::PhastCons9way" do
|
|
1578
|
+
context ".first" do
|
|
1579
|
+
it 'returns the first records' do
|
|
1580
|
+
result = Bio::Ucsc::Rn4::PhastCons9way.first
|
|
1581
|
+
pp result
|
|
1582
|
+
result.should be_true
|
|
1583
|
+
end
|
|
1584
|
+
end
|
|
1585
|
+
end
|
|
1586
|
+
|
|
1587
|
+
describe "Bio::Ucsc::Rn4::PhastConsElements9way" do
|
|
1588
|
+
context ".first" do
|
|
1589
|
+
it 'returns the first records' do
|
|
1590
|
+
result = Bio::Ucsc::Rn4::PhastConsElements9way.first
|
|
1591
|
+
pp result
|
|
1592
|
+
result.should be_true
|
|
1593
|
+
end
|
|
1594
|
+
end
|
|
1595
|
+
end
|
|
1596
|
+
|
|
1597
|
+
describe "Bio::Ucsc::Rn4::ProductName" do
|
|
1598
|
+
context ".first" do
|
|
1599
|
+
it 'returns the first records' do
|
|
1600
|
+
result = Bio::Ucsc::Rn4::ProductName.first
|
|
1601
|
+
pp result
|
|
1602
|
+
result.should be_true
|
|
1603
|
+
end
|
|
1604
|
+
end
|
|
1605
|
+
end
|
|
1606
|
+
|
|
1607
|
+
describe "Bio::Ucsc::Rn4::RefFlat" do
|
|
1608
|
+
context ".first" do
|
|
1609
|
+
it 'returns the first records' do
|
|
1610
|
+
result = Bio::Ucsc::Rn4::RefFlat.first
|
|
1611
|
+
pp result
|
|
1612
|
+
result.should be_true
|
|
1613
|
+
end
|
|
1614
|
+
end
|
|
1615
|
+
end
|
|
1616
|
+
|
|
1617
|
+
describe "Bio::Ucsc::Rn4::RefGene" do
|
|
1618
|
+
context ".first" do
|
|
1619
|
+
it 'returns the first records' do
|
|
1620
|
+
result = Bio::Ucsc::Rn4::RefGene.first
|
|
1621
|
+
pp result
|
|
1622
|
+
result.should be_true
|
|
1623
|
+
end
|
|
1624
|
+
end
|
|
1625
|
+
end
|
|
1626
|
+
|
|
1627
|
+
describe "Bio::Ucsc::Rn4::RefLink" do
|
|
1628
|
+
context ".first" do
|
|
1629
|
+
it 'returns the first records' do
|
|
1630
|
+
result = Bio::Ucsc::Rn4::RefLink.first
|
|
1631
|
+
pp result
|
|
1632
|
+
result.should be_true
|
|
1633
|
+
end
|
|
1634
|
+
end
|
|
1635
|
+
end
|
|
1636
|
+
|
|
1637
|
+
describe "Bio::Ucsc::Rn4::RefSeqAli" do
|
|
1638
|
+
context ".first" do
|
|
1639
|
+
it 'returns the first records' do
|
|
1640
|
+
result = Bio::Ucsc::Rn4::RefSeqAli.first
|
|
1641
|
+
pp result
|
|
1642
|
+
result.should be_true
|
|
1643
|
+
end
|
|
1644
|
+
end
|
|
1645
|
+
end
|
|
1646
|
+
|
|
1647
|
+
describe "Bio::Ucsc::Rn4::RefSeqStatus" do
|
|
1648
|
+
context ".first" do
|
|
1649
|
+
it 'returns the first records' do
|
|
1650
|
+
result = Bio::Ucsc::Rn4::RefSeqStatus.first
|
|
1651
|
+
pp result
|
|
1652
|
+
result.should be_true
|
|
1653
|
+
end
|
|
1654
|
+
end
|
|
1655
|
+
end
|
|
1656
|
+
|
|
1657
|
+
describe "Bio::Ucsc::Rn4::RefSeqSummary" do
|
|
1658
|
+
context ".first" do
|
|
1659
|
+
it 'returns the first records' do
|
|
1660
|
+
result = Bio::Ucsc::Rn4::RefSeqSummary.first
|
|
1661
|
+
pp result
|
|
1662
|
+
result.should be_true
|
|
1663
|
+
end
|
|
1664
|
+
end
|
|
1665
|
+
end
|
|
1666
|
+
|
|
1667
|
+
describe "Bio::Ucsc::Rn4::RgdQtl" do
|
|
1668
|
+
context ".first" do
|
|
1669
|
+
it 'returns the first records' do
|
|
1670
|
+
result = Bio::Ucsc::Rn4::RgdQtl.first
|
|
1671
|
+
pp result
|
|
1672
|
+
result.should be_true
|
|
1673
|
+
end
|
|
1674
|
+
end
|
|
1675
|
+
end
|
|
1676
|
+
|
|
1677
|
+
describe "Bio::Ucsc::Rn4::RgdQtlLink" do
|
|
1678
|
+
context ".first" do
|
|
1679
|
+
it 'returns the first records' do
|
|
1680
|
+
result = Bio::Ucsc::Rn4::RgdQtlLink.first
|
|
1681
|
+
pp result
|
|
1682
|
+
result.should be_true
|
|
1683
|
+
end
|
|
1684
|
+
end
|
|
1685
|
+
end
|
|
1686
|
+
|
|
1687
|
+
describe "Bio::Ucsc::Rn4::Rmsk" do
|
|
1688
|
+
context ".first" do
|
|
1689
|
+
it 'returns the first records' do
|
|
1690
|
+
gi = Bio::GenomicInterval.parse("chrX:1-5,000,000")
|
|
1691
|
+
result = Bio::Ucsc::Rn4::Rmsk.find_by_interval gi
|
|
1692
|
+
pp result
|
|
1693
|
+
result.should be_true
|
|
1694
|
+
end
|
|
1695
|
+
end
|
|
1696
|
+
end
|
|
1697
|
+
|
|
1698
|
+
describe "Bio::Ucsc::Rn4::ScBlastTab" do
|
|
1699
|
+
context ".first" do
|
|
1700
|
+
it 'returns the first records' do
|
|
1701
|
+
result = Bio::Ucsc::Rn4::ScBlastTab.first
|
|
1702
|
+
pp result
|
|
1703
|
+
result.should be_true
|
|
1704
|
+
end
|
|
1705
|
+
end
|
|
1706
|
+
end
|
|
1707
|
+
|
|
1708
|
+
describe "Bio::Ucsc::Rn4::Seq" do
|
|
1709
|
+
context ".first" do
|
|
1710
|
+
it 'returns the first records' do
|
|
1711
|
+
result = Bio::Ucsc::Rn4::Seq.first
|
|
1712
|
+
pp result
|
|
1713
|
+
result.should be_true
|
|
1714
|
+
end
|
|
1715
|
+
end
|
|
1716
|
+
end
|
|
1717
|
+
|
|
1718
|
+
describe "Bio::Ucsc::Rn4::Sex" do
|
|
1719
|
+
context ".first" do
|
|
1720
|
+
it 'returns the first records' do
|
|
1721
|
+
result = Bio::Ucsc::Rn4::Sex.first
|
|
1722
|
+
pp result
|
|
1723
|
+
result.should be_true
|
|
1724
|
+
end
|
|
1725
|
+
end
|
|
1726
|
+
end
|
|
1727
|
+
|
|
1728
|
+
describe "Bio::Ucsc::Rn4::SfAssign" do
|
|
1729
|
+
context ".first" do
|
|
1730
|
+
it 'returns the first records' do
|
|
1731
|
+
result = Bio::Ucsc::Rn4::SfAssign.first
|
|
1732
|
+
pp result
|
|
1733
|
+
result.should be_true
|
|
1734
|
+
end
|
|
1735
|
+
end
|
|
1736
|
+
end
|
|
1737
|
+
|
|
1738
|
+
describe "Bio::Ucsc::Rn4::SfDes" do
|
|
1739
|
+
context ".first" do
|
|
1740
|
+
it 'returns the first records' do
|
|
1741
|
+
result = Bio::Ucsc::Rn4::SfDes.first
|
|
1742
|
+
pp result
|
|
1743
|
+
result.should be_true
|
|
1744
|
+
end
|
|
1745
|
+
end
|
|
1746
|
+
end
|
|
1747
|
+
|
|
1748
|
+
describe "Bio::Ucsc::Rn4::SfDescription" do
|
|
1749
|
+
context ".first" do
|
|
1750
|
+
it 'returns the first records' do
|
|
1751
|
+
result = Bio::Ucsc::Rn4::SfDescription.first
|
|
1752
|
+
pp result
|
|
1753
|
+
result.should be_true
|
|
1754
|
+
end
|
|
1755
|
+
end
|
|
1756
|
+
end
|
|
1757
|
+
|
|
1758
|
+
describe "Bio::Ucsc::Rn4::SgpGene" do
|
|
1759
|
+
context ".first" do
|
|
1760
|
+
it 'returns the first records' do
|
|
1761
|
+
result = Bio::Ucsc::Rn4::SgpGene.first
|
|
1762
|
+
pp result
|
|
1763
|
+
result.should be_true
|
|
1764
|
+
end
|
|
1765
|
+
end
|
|
1766
|
+
end
|
|
1767
|
+
|
|
1768
|
+
describe "Bio::Ucsc::Rn4::SimpleRepeat" do
|
|
1769
|
+
context ".first" do
|
|
1770
|
+
it 'returns the first records' do
|
|
1771
|
+
result = Bio::Ucsc::Rn4::SimpleRepeat.first
|
|
1772
|
+
pp result
|
|
1773
|
+
result.should be_true
|
|
1774
|
+
end
|
|
1775
|
+
end
|
|
1776
|
+
end
|
|
1777
|
+
|
|
1778
|
+
describe "Bio::Ucsc::Rn4::Snp125" do
|
|
1779
|
+
context ".first" do
|
|
1780
|
+
it 'returns the first records' do
|
|
1781
|
+
result = Bio::Ucsc::Rn4::Snp125.first
|
|
1782
|
+
pp result
|
|
1783
|
+
result.should be_true
|
|
1784
|
+
end
|
|
1785
|
+
end
|
|
1786
|
+
end
|
|
1787
|
+
|
|
1788
|
+
describe "Bio::Ucsc::Rn4::Snp125ExceptionDesc" do
|
|
1789
|
+
context ".first" do
|
|
1790
|
+
it 'returns the first records' do
|
|
1791
|
+
result = Bio::Ucsc::Rn4::Snp125ExceptionDesc.first
|
|
1792
|
+
pp result
|
|
1793
|
+
result.should be_true
|
|
1794
|
+
end
|
|
1795
|
+
end
|
|
1796
|
+
end
|
|
1797
|
+
|
|
1798
|
+
describe "Bio::Ucsc::Rn4::Snp125Exceptions" do
|
|
1799
|
+
context ".first" do
|
|
1800
|
+
it 'returns the first records' do
|
|
1801
|
+
result = Bio::Ucsc::Rn4::Snp125Exceptions.first
|
|
1802
|
+
pp result
|
|
1803
|
+
result.should be_true
|
|
1804
|
+
end
|
|
1805
|
+
end
|
|
1806
|
+
end
|
|
1807
|
+
|
|
1808
|
+
describe "Bio::Ucsc::Rn4::SnpSeq" do
|
|
1809
|
+
context ".first" do
|
|
1810
|
+
it 'returns the first records' do
|
|
1811
|
+
result = Bio::Ucsc::Rn4::SnpSeq.first
|
|
1812
|
+
pp result
|
|
1813
|
+
result.should be_true
|
|
1814
|
+
end
|
|
1815
|
+
end
|
|
1816
|
+
end
|
|
1817
|
+
|
|
1818
|
+
describe "Bio::Ucsc::Rn4::Source" do
|
|
1819
|
+
context ".first" do
|
|
1820
|
+
it 'returns the first records' do
|
|
1821
|
+
result = Bio::Ucsc::Rn4::Source.first
|
|
1822
|
+
pp result
|
|
1823
|
+
result.should be_true
|
|
1824
|
+
end
|
|
1825
|
+
end
|
|
1826
|
+
end
|
|
1827
|
+
|
|
1828
|
+
describe "Bio::Ucsc::Rn4::SpMrna" do
|
|
1829
|
+
context ".first" do
|
|
1830
|
+
it 'returns the first records' do
|
|
1831
|
+
result = Bio::Ucsc::Rn4::SpMrna.first
|
|
1832
|
+
pp result
|
|
1833
|
+
result.should be_true
|
|
1834
|
+
end
|
|
1835
|
+
end
|
|
1836
|
+
end
|
|
1837
|
+
|
|
1838
|
+
describe "Bio::Ucsc::Rn4::StsAlias" do
|
|
1839
|
+
context ".first" do
|
|
1840
|
+
it 'returns the first records' do
|
|
1841
|
+
result = Bio::Ucsc::Rn4::StsAlias.first
|
|
1842
|
+
pp result
|
|
1843
|
+
result.should be_true
|
|
1844
|
+
end
|
|
1845
|
+
end
|
|
1846
|
+
end
|
|
1847
|
+
|
|
1848
|
+
describe "Bio::Ucsc::Rn4::StsInfoRat" do
|
|
1849
|
+
context ".first" do
|
|
1850
|
+
it 'returns the first records' do
|
|
1851
|
+
result = Bio::Ucsc::Rn4::StsInfoRat.first
|
|
1852
|
+
pp result
|
|
1853
|
+
result.should be_true
|
|
1854
|
+
end
|
|
1855
|
+
end
|
|
1856
|
+
end
|
|
1857
|
+
|
|
1858
|
+
describe "Bio::Ucsc::Rn4::StsMapRat" do
|
|
1859
|
+
context ".first" do
|
|
1860
|
+
it 'returns the first records' do
|
|
1861
|
+
result = Bio::Ucsc::Rn4::StsMapRat.first
|
|
1862
|
+
pp result
|
|
1863
|
+
result.should be_true
|
|
1864
|
+
end
|
|
1865
|
+
end
|
|
1866
|
+
end
|
|
1867
|
+
|
|
1868
|
+
describe "Bio::Ucsc::Rn4::TRNAs" do
|
|
1869
|
+
context ".first" do
|
|
1870
|
+
it 'returns the first records' do
|
|
1871
|
+
result = Bio::Ucsc::Rn4::TRNAs.first
|
|
1872
|
+
pp result
|
|
1873
|
+
result.should be_true
|
|
1874
|
+
end
|
|
1875
|
+
end
|
|
1876
|
+
end
|
|
1877
|
+
|
|
1878
|
+
describe "Bio::Ucsc::Rn4::TableDescriptions" do
|
|
1879
|
+
context ".first" do
|
|
1880
|
+
it 'returns the first records' do
|
|
1881
|
+
result = Bio::Ucsc::Rn4::TableDescriptions.first
|
|
1882
|
+
pp result
|
|
1883
|
+
result.should be_true
|
|
1884
|
+
end
|
|
1885
|
+
end
|
|
1886
|
+
end
|
|
1887
|
+
|
|
1888
|
+
describe "Bio::Ucsc::Rn4::Tissue" do
|
|
1889
|
+
context ".first" do
|
|
1890
|
+
it 'returns the first records' do
|
|
1891
|
+
result = Bio::Ucsc::Rn4::Tissue.first
|
|
1892
|
+
pp result
|
|
1893
|
+
result.should be_true
|
|
1894
|
+
end
|
|
1895
|
+
end
|
|
1896
|
+
end
|
|
1897
|
+
|
|
1898
|
+
describe "Bio::Ucsc::Rn4::TrackDb" do
|
|
1899
|
+
context ".first" do
|
|
1900
|
+
it 'returns the first records' do
|
|
1901
|
+
result = Bio::Ucsc::Rn4::TrackDb.first
|
|
1902
|
+
pp result
|
|
1903
|
+
result.should be_true
|
|
1904
|
+
end
|
|
1905
|
+
end
|
|
1906
|
+
end
|
|
1907
|
+
|
|
1908
|
+
describe "Bio::Ucsc::Rn4::TransMapAlnMRna" do
|
|
1909
|
+
context ".first" do
|
|
1910
|
+
it 'returns the first records' do
|
|
1911
|
+
result = Bio::Ucsc::Rn4::TransMapAlnMRna.first
|
|
1912
|
+
pp result
|
|
1913
|
+
result.should be_true
|
|
1914
|
+
end
|
|
1915
|
+
end
|
|
1916
|
+
end
|
|
1917
|
+
|
|
1918
|
+
describe "Bio::Ucsc::Rn4::TransMapAlnRefSeq" do
|
|
1919
|
+
context ".first" do
|
|
1920
|
+
it 'returns the first records' do
|
|
1921
|
+
result = Bio::Ucsc::Rn4::TransMapAlnRefSeq.first
|
|
1922
|
+
pp result
|
|
1923
|
+
result.should be_true
|
|
1924
|
+
end
|
|
1925
|
+
end
|
|
1926
|
+
end
|
|
1927
|
+
|
|
1928
|
+
describe "Bio::Ucsc::Rn4::TransMapAlnSplicedEst" do
|
|
1929
|
+
context ".first" do
|
|
1930
|
+
it 'returns the first records' do
|
|
1931
|
+
result = Bio::Ucsc::Rn4::TransMapAlnSplicedEst.first
|
|
1932
|
+
pp result
|
|
1933
|
+
result.should be_true
|
|
1934
|
+
end
|
|
1935
|
+
end
|
|
1936
|
+
end
|
|
1937
|
+
|
|
1938
|
+
describe "Bio::Ucsc::Rn4::TransMapAlnUcscGenes" do
|
|
1939
|
+
context ".first" do
|
|
1940
|
+
it 'returns the first records' do
|
|
1941
|
+
result = Bio::Ucsc::Rn4::TransMapAlnUcscGenes.first
|
|
1942
|
+
pp result
|
|
1943
|
+
result.should be_true
|
|
1944
|
+
end
|
|
1945
|
+
end
|
|
1946
|
+
end
|
|
1947
|
+
|
|
1948
|
+
describe "Bio::Ucsc::Rn4::TransMapInfoMRna" do
|
|
1949
|
+
context ".first" do
|
|
1950
|
+
it 'returns the first records' do
|
|
1951
|
+
result = Bio::Ucsc::Rn4::TransMapInfoMRna.first
|
|
1952
|
+
pp result
|
|
1953
|
+
result.should be_true
|
|
1954
|
+
end
|
|
1955
|
+
end
|
|
1956
|
+
end
|
|
1957
|
+
|
|
1958
|
+
describe "Bio::Ucsc::Rn4::TransMapInfoRefSeq" do
|
|
1959
|
+
context ".first" do
|
|
1960
|
+
it 'returns the first records' do
|
|
1961
|
+
result = Bio::Ucsc::Rn4::TransMapInfoRefSeq.first
|
|
1962
|
+
pp result
|
|
1963
|
+
result.should be_true
|
|
1964
|
+
end
|
|
1965
|
+
end
|
|
1966
|
+
end
|
|
1967
|
+
|
|
1968
|
+
describe "Bio::Ucsc::Rn4::TransMapInfoSplicedEst" do
|
|
1969
|
+
context ".first" do
|
|
1970
|
+
it 'returns the first records' do
|
|
1971
|
+
result = Bio::Ucsc::Rn4::TransMapInfoSplicedEst.first
|
|
1972
|
+
pp result
|
|
1973
|
+
result.should be_true
|
|
1974
|
+
end
|
|
1975
|
+
end
|
|
1976
|
+
end
|
|
1977
|
+
|
|
1978
|
+
describe "Bio::Ucsc::Rn4::TransMapInfoUcscGenes" do
|
|
1979
|
+
context ".first" do
|
|
1980
|
+
it 'returns the first records' do
|
|
1981
|
+
result = Bio::Ucsc::Rn4::TransMapInfoUcscGenes.first
|
|
1982
|
+
pp result
|
|
1983
|
+
result.should be_true
|
|
1984
|
+
end
|
|
1985
|
+
end
|
|
1986
|
+
end
|
|
1987
|
+
|
|
1988
|
+
describe "Bio::Ucsc::Rn4::WgEncodeNhgriBip" do
|
|
1989
|
+
context ".first" do
|
|
1990
|
+
it 'returns the first records' do
|
|
1991
|
+
result = Bio::Ucsc::Rn4::WgEncodeNhgriBip.first
|
|
1992
|
+
pp result
|
|
1993
|
+
result.should be_true
|
|
1994
|
+
end
|
|
1995
|
+
end
|
|
1996
|
+
end
|
|
1997
|
+
|
|
1998
|
+
describe "Bio::Ucsc::Rn4::XenoMrna" do
|
|
1999
|
+
context ".first" do
|
|
2000
|
+
it 'returns the first records' do
|
|
2001
|
+
result = Bio::Ucsc::Rn4::XenoMrna.first
|
|
2002
|
+
pp result
|
|
2003
|
+
result.should be_true
|
|
2004
|
+
end
|
|
2005
|
+
end
|
|
2006
|
+
end
|
|
2007
|
+
|
|
2008
|
+
describe "Bio::Ucsc::Rn4::XenoRefFlat" do
|
|
2009
|
+
context ".first" do
|
|
2010
|
+
it 'returns the first records' do
|
|
2011
|
+
result = Bio::Ucsc::Rn4::XenoRefFlat.first
|
|
2012
|
+
pp result
|
|
2013
|
+
result.should be_true
|
|
2014
|
+
end
|
|
2015
|
+
end
|
|
2016
|
+
end
|
|
2017
|
+
|
|
2018
|
+
describe "Bio::Ucsc::Rn4::XenoRefGene" do
|
|
2019
|
+
context ".first" do
|
|
2020
|
+
it 'returns the first records' do
|
|
2021
|
+
result = Bio::Ucsc::Rn4::XenoRefGene.first
|
|
2022
|
+
pp result
|
|
2023
|
+
result.should be_true
|
|
2024
|
+
end
|
|
2025
|
+
end
|
|
2026
|
+
end
|
|
2027
|
+
|
|
2028
|
+
describe "Bio::Ucsc::Rn4::XenoRefSeqAli" do
|
|
2029
|
+
context ".first" do
|
|
2030
|
+
it 'returns the first records' do
|
|
2031
|
+
result = Bio::Ucsc::Rn4::XenoRefSeqAli.first
|
|
2032
|
+
pp result
|
|
2033
|
+
result.should be_true
|
|
2034
|
+
end
|
|
2035
|
+
end
|
|
2036
|
+
end
|
|
2037
|
+
|
|
2038
|
+
end
|