bio-ucsc-api 0.2.0 → 0.2.1
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- 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
@@ -0,0 +1,81 @@
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# Copyright::
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# Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
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# License:: The Ruby licence (Ryby's / GPLv2 dual)
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#
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# In the hg18 database, this table is actually separated
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# into "chr1_*", "chr2_*", etc. This class dynamically
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# define *::Chr1_*, *::Chr2_*, etc. The
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# Rmsk.find_by_interval calls an appropreate class automatically.
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module Bio
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module Ucsc
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module SusScr2
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class Mrna
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KLASS = "Mrna"
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KLASS_S = "mrna"
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Bio::Ucsc::SusScr2::CHROMS.each do |chr|
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class_eval %!
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class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
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set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
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set_primary_key nil
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set_inheritance_column nil
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def self.find_by_interval(interval, opt = {:partial => true})
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find_first_or_all_by_interval(interval, :first, opt)
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end
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def self.find_all_by_interval(interval, opt = {:partial => true})
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find_first_or_all_by_interval(interval, :all, opt)
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end
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def self.find_first_or_all_by_interval(interval, first_all, opt)
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zstart = interval.zero_start
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zend = interval.zero_end
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if opt[:partial] == true
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where = <<-SQL
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tName = :chrom
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AND bin in (:bins)
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AND ((tStart BETWEEN :zstart AND :zend)
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OR (tEnd BETWEEN :zstart AND :zend)
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OR (tStart <= :zstart AND tEnd >= :zend))
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SQL
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else
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where = <<-SQL
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tName = :chrom
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AND bin in (:bins)
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AND ((tStart BETWEEN :zstart AND :zend)
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AND (tEnd BETWEEN :zstart AND :zend))
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SQL
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end
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cond = {
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:chrom => interval.chrom,
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:bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
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:zstart => zstart,
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:zend => zend,
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}
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self.find(first_all,
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{ :select => "*",
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:conditions => [where, cond], })
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end
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end
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!
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end # each chromosome
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def self.find_by_interval(interval, opt = {:partial => true})
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chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
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chr_klass = self.const_get("#{chrom}_#{KLASS}")
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chr_klass.__send__(:find_by_interval, interval, opt)
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end
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def self.find_all_by_interval(interval, opt = {:partial => true})
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chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
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chr_klass = self.const_get("#{chrom}_#{KLASS}")
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chr_klass.__send__(:find_all_by_interval, interval, opt)
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end
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end # class
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end # module Hg18
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end # module Ucsc
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end # module Bio
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-
|
406
|
-
)
|
401
|
+
{ :select => "*",
|
402
|
+
:conditions => [where, cond], })
|
407
403
|
end
|
408
404
|
end
|
409
405
|
!
|
@@ -444,8 +440,8 @@ AND ((genoStart BETWEEN :zstart AND :zend)
|
|
444
440
|
:zend => zend,
|
445
441
|
}
|
446
442
|
self.find(first_all,
|
447
|
-
:select => "*",
|
448
|
-
|
443
|
+
{ :select => "*",
|
444
|
+
:conditions => [where, cond], })
|
449
445
|
end
|
450
446
|
end
|
451
447
|
!
|
@@ -465,14 +461,14 @@ AND ((genoStart BETWEEN :zstart AND :zend)
|
|
465
461
|
end
|
466
462
|
|
467
463
|
def uphead(sym)
|
468
|
-
(sym.to_s[0..0].upcase + sym[1..-1])
|
464
|
+
(sym.to_s[0..0].upcase + sym.to_s[1..-1])
|
469
465
|
end
|
470
466
|
|
471
467
|
def downhead(sym)
|
472
468
|
if UPPERCASED_TABLE_PREFIX.any?{|x|sym.to_s.start_with? x}
|
473
469
|
sym.to_s
|
474
470
|
else
|
475
|
-
(sym.to_s[0..0].downcase + sym[1..-1])
|
471
|
+
(sym.to_s[0..0].downcase + sym.to_s[1..-1])
|
476
472
|
end
|
477
473
|
end
|
478
474
|
|
@@ -0,0 +1,33 @@
|
|
1
|
+
#
|
2
|
+
# = AUTOMATIC Table Definition of the Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) assembly
|
3
|
+
# Copyright:: Copyright (C) 2011
|
4
|
+
# MISHIMA, Hiroyuki
|
5
|
+
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
+
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
7
|
+
#
|
8
|
+
|
9
|
+
require "#{File.dirname(__FILE__)}/taegut1/db_connection"
|
10
|
+
require "#{File.dirname(__FILE__)}/table_class_detector"
|
11
|
+
|
12
|
+
module Bio
|
13
|
+
module Ucsc
|
14
|
+
module TaeGut1
|
15
|
+
CHROMS =
|
16
|
+
%w(chr1 chr1A chr1B chr2 chr3 chr4 chr4A chr5 chr6 chr7 chr8 chr9 chr10
|
17
|
+
chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
|
18
|
+
chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chrZ chrM)
|
19
|
+
|
20
|
+
extend TableClassDetector
|
21
|
+
|
22
|
+
base = "#{File.dirname(__FILE__)}/taegut1"
|
23
|
+
autoload :ChainGalGal3, "#{base}/chaingalgal3"
|
24
|
+
autoload :ChainGalGal3Link, "#{base}/chaingalgal3link"
|
25
|
+
autoload :Est, "#{base}/est"
|
26
|
+
autoload :Gap, "#{base}/gap"
|
27
|
+
autoload :Gold, "#{base}/gold"
|
28
|
+
autoload :IntronEst, "#{base}/intronest"
|
29
|
+
autoload :Mrna, "#{base}/mrna"
|
30
|
+
autoload :Rmsk, "#{base}/rmsk"
|
31
|
+
end
|
32
|
+
end
|
33
|
+
end
|
@@ -0,0 +1,81 @@
|
|
1
|
+
# Copyright::
|
2
|
+
# Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
3
|
+
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
4
|
+
#
|
5
|
+
# In the hg18 database, this table is actually separated
|
6
|
+
# into "chr1_*", "chr2_*", etc. This class dynamically
|
7
|
+
# define *::Chr1_*, *::Chr2_*, etc. The
|
8
|
+
# Rmsk.find_by_interval calls an appropreate class automatically.
|
9
|
+
|
10
|
+
module Bio
|
11
|
+
module Ucsc
|
12
|
+
module TaeGut1
|
13
|
+
|
14
|
+
class ChainGalGal3
|
15
|
+
KLASS = "ChainGalGal3"
|
16
|
+
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
|
+
|
18
|
+
Bio::Ucsc::GalGal3::CHROMS.each do |chr|
|
19
|
+
class_eval %!
|
20
|
+
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
+
set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
22
|
+
set_primary_key nil
|
23
|
+
set_inheritance_column nil
|
24
|
+
|
25
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
26
|
+
find_first_or_all_by_interval(interval, :first, opt)
|
27
|
+
end
|
28
|
+
|
29
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
30
|
+
find_first_or_all_by_interval(interval, :all, opt)
|
31
|
+
end
|
32
|
+
|
33
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
34
|
+
zstart = interval.zero_start
|
35
|
+
zend = interval.zero_end
|
36
|
+
if opt[:partial] == true
|
37
|
+
where = <<-SQL
|
38
|
+
tName = :chrom
|
39
|
+
AND bin in (:bins)
|
40
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
41
|
+
OR (tEnd BETWEEN :zstart AND :zend)
|
42
|
+
OR (tStart <= :zstart AND tEnd >= :zend))
|
43
|
+
SQL
|
44
|
+
else
|
45
|
+
where = <<-SQL
|
46
|
+
tName = :chrom
|
47
|
+
AND bin in (:bins)
|
48
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
49
|
+
AND (tEnd BETWEEN :zstart AND :zend))
|
50
|
+
SQL
|
51
|
+
end
|
52
|
+
cond = {
|
53
|
+
:chrom => interval.chrom,
|
54
|
+
:bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
|
55
|
+
:zstart => zstart,
|
56
|
+
:zend => zend,
|
57
|
+
}
|
58
|
+
self.find(first_all,
|
59
|
+
{ :select => "*",
|
60
|
+
:conditions => [where, cond], })
|
61
|
+
end
|
62
|
+
end
|
63
|
+
!
|
64
|
+
end # each chromosome
|
65
|
+
|
66
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
67
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
|
+
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
|
+
end
|
71
|
+
|
72
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
73
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
|
+
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
76
|
+
end
|
77
|
+
end # class
|
78
|
+
|
79
|
+
end # module Hg18
|
80
|
+
end # module Ucsc
|
81
|
+
end # module Bio
|
@@ -0,0 +1,81 @@
|
|
1
|
+
# Copyright::
|
2
|
+
# Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
3
|
+
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
4
|
+
#
|
5
|
+
# In the hg18 database, this table is actually separated
|
6
|
+
# into "chr1_*", "chr2_*", etc. This class dynamically
|
7
|
+
# define *::Chr1_*, *::Chr2_*, etc. The
|
8
|
+
# Rmsk.find_by_interval calls an appropreate class automatically.
|
9
|
+
|
10
|
+
module Bio
|
11
|
+
module Ucsc
|
12
|
+
module TaeGut1
|
13
|
+
|
14
|
+
class ChainGalGal3Link
|
15
|
+
KLASS = "ChainGalGal3Link"
|
16
|
+
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
|
+
|
18
|
+
Bio::Ucsc::GalGal3::CHROMS.each do |chr|
|
19
|
+
class_eval %!
|
20
|
+
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
+
set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
22
|
+
set_primary_key nil
|
23
|
+
set_inheritance_column nil
|
24
|
+
|
25
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
26
|
+
find_first_or_all_by_interval(interval, :first, opt)
|
27
|
+
end
|
28
|
+
|
29
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
30
|
+
find_first_or_all_by_interval(interval, :all, opt)
|
31
|
+
end
|
32
|
+
|
33
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
34
|
+
zstart = interval.zero_start
|
35
|
+
zend = interval.zero_end
|
36
|
+
if opt[:partial] == true
|
37
|
+
where = <<-SQL
|
38
|
+
tName = :chrom
|
39
|
+
AND bin in (:bins)
|
40
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
41
|
+
OR (tEnd BETWEEN :zstart AND :zend)
|
42
|
+
OR (tStart <= :zstart AND tEnd >= :zend))
|
43
|
+
SQL
|
44
|
+
else
|
45
|
+
where = <<-SQL
|
46
|
+
tName = :chrom
|
47
|
+
AND bin in (:bins)
|
48
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
49
|
+
AND (tEnd BETWEEN :zstart AND :zend))
|
50
|
+
SQL
|
51
|
+
end
|
52
|
+
cond = {
|
53
|
+
:chrom => interval.chrom,
|
54
|
+
:bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
|
55
|
+
:zstart => zstart,
|
56
|
+
:zend => zend,
|
57
|
+
}
|
58
|
+
self.find(first_all,
|
59
|
+
{ :select => "*",
|
60
|
+
:conditions => [where, cond], })
|
61
|
+
end
|
62
|
+
end
|
63
|
+
!
|
64
|
+
end # each chromosome
|
65
|
+
|
66
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
67
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
|
+
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
|
+
end
|
71
|
+
|
72
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
73
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
|
+
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
76
|
+
end
|
77
|
+
end # class
|
78
|
+
|
79
|
+
end # module Hg18
|
80
|
+
end # module Ucsc
|
81
|
+
end # module Bio
|
@@ -0,0 +1,57 @@
|
|
1
|
+
#
|
2
|
+
# = db_connection.rb - UCSC DB connection
|
3
|
+
#
|
4
|
+
# Copyright:: Cioyrught (C) 2011
|
5
|
+
# MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
+
# Copyright:: Copyright (C) 2010
|
7
|
+
# Jan Aerts <jan.aerts@gmail.com>
|
8
|
+
# License:: Ruby licence (Ryby's / GPLv2 dual)
|
9
|
+
|
10
|
+
require 'rubygems'
|
11
|
+
require 'active_record'
|
12
|
+
|
13
|
+
module Bio
|
14
|
+
module Ucsc
|
15
|
+
|
16
|
+
module TaeGut1
|
17
|
+
DATABASE_NAME = "taeGut1"
|
18
|
+
|
19
|
+
# = DESCRIPTION
|
20
|
+
# Actual connection established to the UCSC mysql server.
|
21
|
+
class DBConnection < ActiveRecord::Base
|
22
|
+
# = DESCRIPTION
|
23
|
+
# The #connect method make the connection
|
24
|
+
#
|
25
|
+
# = USAGE
|
26
|
+
# Bin::Ucsc::DB_NAME::DBConnection.connect
|
27
|
+
#
|
28
|
+
# ---
|
29
|
+
# *Arguments*: none
|
30
|
+
@@db_adapter ||= 'mysql'
|
31
|
+
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
32
|
+
@@db_username ||= 'genome'
|
33
|
+
@@db_password ||= ''
|
34
|
+
|
35
|
+
cattr_accessor :db_adapter, :db_host, :db_username, :db_password
|
36
|
+
|
37
|
+
self.abstract_class = true
|
38
|
+
|
39
|
+
def self.default
|
40
|
+
@@db_adapter = 'mysql'
|
41
|
+
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
42
|
+
@@db_username = 'genome'
|
43
|
+
@@db_password = ''
|
44
|
+
end
|
45
|
+
|
46
|
+
def self.connect
|
47
|
+
establish_connection({ :adapter => @@db_adapter,
|
48
|
+
:host => @@db_host,
|
49
|
+
:database => DATABASE_NAME,
|
50
|
+
:username => @@db_username,
|
51
|
+
:password => @@db_password, })
|
52
|
+
end
|
53
|
+
end
|
54
|
+
end # module
|
55
|
+
|
56
|
+
end # module Ucsc
|
57
|
+
end # module Bio
|
@@ -0,0 +1,81 @@
|
|
1
|
+
# Copyright::
|
2
|
+
# Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
3
|
+
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
4
|
+
#
|
5
|
+
# In the hg18 database, this table is actually separated
|
6
|
+
# into "chr1_*", "chr2_*", etc. This class dynamically
|
7
|
+
# define *::Chr1_*, *::Chr2_*, etc. The
|
8
|
+
# Rmsk.find_by_interval calls an appropreate class automatically.
|
9
|
+
|
10
|
+
module Bio
|
11
|
+
module Ucsc
|
12
|
+
module TaeGut1
|
13
|
+
|
14
|
+
class Est
|
15
|
+
KLASS = "Est"
|
16
|
+
KLASS_S = "est"
|
17
|
+
|
18
|
+
Bio::Ucsc::TaeGut1::CHROMS.each do |chr|
|
19
|
+
class_eval %!
|
20
|
+
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
+
set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
22
|
+
set_primary_key nil
|
23
|
+
set_inheritance_column nil
|
24
|
+
|
25
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
26
|
+
find_first_or_all_by_interval(interval, :first, opt)
|
27
|
+
end
|
28
|
+
|
29
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
30
|
+
find_first_or_all_by_interval(interval, :all, opt)
|
31
|
+
end
|
32
|
+
|
33
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
34
|
+
zstart = interval.zero_start
|
35
|
+
zend = interval.zero_end
|
36
|
+
if opt[:partial] == true
|
37
|
+
where = <<-SQL
|
38
|
+
tName = :chrom
|
39
|
+
AND bin in (:bins)
|
40
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
41
|
+
OR (tEnd BETWEEN :zstart AND :zend)
|
42
|
+
OR (tStart <= :zstart AND tEnd >= :zend))
|
43
|
+
SQL
|
44
|
+
else
|
45
|
+
where = <<-SQL
|
46
|
+
tName = :chrom
|
47
|
+
AND bin in (:bins)
|
48
|
+
AND ((tStart BETWEEN :zstart AND :zend)
|
49
|
+
AND (tEnd BETWEEN :zstart AND :zend))
|
50
|
+
SQL
|
51
|
+
end
|
52
|
+
cond = {
|
53
|
+
:chrom => interval.chrom,
|
54
|
+
:bins => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
|
55
|
+
:zstart => zstart,
|
56
|
+
:zend => zend,
|
57
|
+
}
|
58
|
+
self.find(first_all,
|
59
|
+
{ :select => "*",
|
60
|
+
:conditions => [where, cond], })
|
61
|
+
end
|
62
|
+
end
|
63
|
+
!
|
64
|
+
end # each chromosome
|
65
|
+
|
66
|
+
def self.find_by_interval(interval, opt = {:partial => true})
|
67
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
|
+
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
|
+
end
|
71
|
+
|
72
|
+
def self.find_all_by_interval(interval, opt = {:partial => true})
|
73
|
+
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
|
+
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
|
+
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
76
|
+
end
|
77
|
+
end # class
|
78
|
+
|
79
|
+
end # module Hg18
|
80
|
+
end # module Ucsc
|
81
|
+
end # module Bio
|