bio-ucsc-api 0.3.1 → 0.4.0
Sign up to get free protection for your applications and to get access to all the features.
- data/Gemfile +4 -3
- data/Gemfile.lock +31 -20
- data/README.md +224 -0
- data/Rakefile +5 -8
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +39 -122
- data/lib/bio-ucsc.rb +10 -5
- data/lib/bio-ucsc/ailmel1.rb +5 -3
- data/lib/bio-ucsc/anocar2.rb +7 -6
- data/lib/bio-ucsc/anogam1.rb +7 -5
- data/lib/bio-ucsc/anogam1/chaindm3.rb +11 -8
- data/lib/bio-ucsc/anogam1/chaindm3link.rb +11 -8
- data/lib/bio-ucsc/anogam1/est.rb +11 -8
- data/lib/bio-ucsc/anogam1/gap.rb +11 -8
- data/lib/bio-ucsc/anogam1/gold.rb +11 -8
- data/lib/bio-ucsc/anogam1/intronest.rb +11 -8
- data/lib/bio-ucsc/anogam1/mrna.rb +11 -8
- data/lib/bio-ucsc/anogam1/rmsk.rb +10 -7
- data/lib/bio-ucsc/apimel2.rb +5 -3
- data/lib/bio-ucsc/apimel2/chaindm2.rb +11 -8
- data/lib/bio-ucsc/apimel2/chaindm2link.rb +11 -8
- data/lib/bio-ucsc/aplcal1.rb +5 -3
- data/lib/bio-ucsc/aplcal1/chaincaepb1.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaincaepb1link.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaincaerem2.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaincaerem2link.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaincb3.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaincb3link.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaince6.rb +11 -8
- data/lib/bio-ucsc/aplcal1/chaince6link.rb +11 -8
- data/lib/bio-ucsc/aplcal1/gap.rb +11 -8
- data/lib/bio-ucsc/aplcal1/gold.rb +11 -8
- data/lib/bio-ucsc/aplcal1/rmsk.rb +10 -7
- data/lib/bio-ucsc/bostau4.rb +5 -3
- data/lib/bio-ucsc/braflo1.rb +5 -3
- data/lib/bio-ucsc/braflo1/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/braflo1/chaingalgal3link.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainhg18.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainhg18link.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainmm9.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainpetmar1.rb +11 -8
- data/lib/bio-ucsc/braflo1/chainpetmar1link.rb +11 -8
- data/lib/bio-ucsc/braflo1/gap.rb +11 -8
- data/lib/bio-ucsc/braflo1/gold.rb +11 -8
- data/lib/bio-ucsc/caejap1.rb +5 -3
- data/lib/bio-ucsc/caejap1/chaince6.rb +11 -8
- data/lib/bio-ucsc/caejap1/chaince6link.rb +11 -8
- data/lib/bio-ucsc/caejap1/gap.rb +11 -8
- data/lib/bio-ucsc/caejap1/gold.rb +11 -8
- data/lib/bio-ucsc/caepb2.rb +6 -4
- data/lib/bio-ucsc/caepb2/chaince6.rb +11 -8
- data/lib/bio-ucsc/caepb2/chaince6link.rb +11 -8
- data/lib/bio-ucsc/caepb2/gap.rb +11 -8
- data/lib/bio-ucsc/caepb2/gold.rb +11 -8
- data/lib/bio-ucsc/caerem3.rb +5 -3
- data/lib/bio-ucsc/caerem3/chaince6.rb +11 -8
- data/lib/bio-ucsc/caerem3/chaince6link.rb +11 -8
- data/lib/bio-ucsc/caerem3/gap.rb +11 -8
- data/lib/bio-ucsc/caerem3/gold.rb +11 -8
- data/lib/bio-ucsc/caljac3.rb +7 -4
- data/lib/bio-ucsc/canfam2.rb +5 -3
- data/lib/bio-ucsc/canfam2/chainbostau4.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainbostau4link.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainmm9.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainrn4.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainrn4link.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainself.rb +11 -8
- data/lib/bio-ucsc/canfam2/chainselflink.rb +11 -8
- data/lib/bio-ucsc/canfam2/est.rb +11 -8
- data/lib/bio-ucsc/canfam2/gap.rb +11 -8
- data/lib/bio-ucsc/canfam2/gold.rb +11 -8
- data/lib/bio-ucsc/canfam2/intronest.rb +11 -8
- data/lib/bio-ucsc/canfam2/mrna.rb +11 -8
- data/lib/bio-ucsc/canfam2/rmsk.rb +10 -7
- data/lib/bio-ucsc/cavpor3.rb +6 -4
- data/lib/bio-ucsc/cb3.rb +5 -3
- data/lib/bio-ucsc/cb3/chaincaepb1.rb +11 -8
- data/lib/bio-ucsc/cb3/chaincaepb1link.rb +11 -8
- data/lib/bio-ucsc/cb3/chaincaerem2.rb +11 -8
- data/lib/bio-ucsc/cb3/chaincaerem2link.rb +11 -8
- data/lib/bio-ucsc/cb3/chaince6.rb +11 -8
- data/lib/bio-ucsc/cb3/chaince6link.rb +11 -8
- data/lib/bio-ucsc/cb3/chainpripac1.rb +11 -8
- data/lib/bio-ucsc/cb3/chainpripac1link.rb +11 -8
- data/lib/bio-ucsc/cb3/est.rb +11 -8
- data/lib/bio-ucsc/cb3/gap.rb +11 -8
- data/lib/bio-ucsc/cb3/gold.rb +11 -8
- data/lib/bio-ucsc/cb3/intronest.rb +11 -8
- data/lib/bio-ucsc/cb3/mrna.rb +11 -8
- data/lib/bio-ucsc/cb3/rmsk.rb +10 -7
- data/lib/bio-ucsc/ce6.rb +8 -4
- data/lib/bio-ucsc/ce6/chaincaejap1.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincaejap1link.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincaepb2.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincaepb2link.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincaerem3.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincaerem3link.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincb3.rb +11 -8
- data/lib/bio-ucsc/ce6/chaincb3link.rb +11 -8
- data/lib/bio-ucsc/ce6/chainpripac1.rb +11 -8
- data/lib/bio-ucsc/ce6/chainpripac1link.rb +11 -8
- data/lib/bio-ucsc/ce6/chainself.rb +11 -8
- data/lib/bio-ucsc/ce6/chainselflink.rb +11 -8
- data/lib/bio-ucsc/ce6/est.rb +11 -8
- data/lib/bio-ucsc/ce6/gap.rb +11 -8
- data/lib/bio-ucsc/ce6/gold.rb +11 -8
- data/lib/bio-ucsc/ce6/intronest.rb +11 -8
- data/lib/bio-ucsc/ce6/mrna.rb +11 -8
- data/lib/bio-ucsc/ce6/rmsk.rb +11 -8
- data/lib/bio-ucsc/ce6/t25mersrepeats.rb +7 -4
- data/lib/bio-ucsc/ci2.rb +6 -3
- data/lib/bio-ucsc/danrer7.rb +6 -3
- data/lib/bio-ucsc/{apimel2/db_connection.rb → db_connector.rb} +33 -23
- data/lib/bio-ucsc/dm3.rb +6 -4
- data/lib/bio-ucsc/dm3/chainanogam1.rb +11 -8
- data/lib/bio-ucsc/dm3/chainanogam1link.rb +11 -8
- data/lib/bio-ucsc/dm3/chainapimel3.rb +11 -8
- data/lib/bio-ucsc/dm3/chainapimel3link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindp3.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindp3link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroana2.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroana2link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroere1.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroere1link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroper1.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroper1link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindrosec1.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindrosec1link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindrosim1.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindrosim1link.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroyak2.rb +11 -8
- data/lib/bio-ucsc/dm3/chaindroyak2link.rb +11 -8
- data/lib/bio-ucsc/dm3/est.rb +11 -8
- data/lib/bio-ucsc/dm3/gap.rb +11 -8
- data/lib/bio-ucsc/dm3/gold.rb +11 -8
- data/lib/bio-ucsc/dm3/intronest.rb +11 -8
- data/lib/bio-ucsc/dm3/mrna.rb +11 -8
- data/lib/bio-ucsc/dm3/rmsk.rb +11 -8
- data/lib/bio-ucsc/dp3.rb +6 -4
- data/lib/bio-ucsc/dp3/chaindm3.rb +11 -8
- data/lib/bio-ucsc/dp3/chaindm3link.rb +11 -8
- data/lib/bio-ucsc/dp3/est.rb +11 -8
- data/lib/bio-ucsc/dp3/gap.rb +11 -8
- data/lib/bio-ucsc/dp3/gold.rb +11 -8
- data/lib/bio-ucsc/dp3/intronest.rb +11 -8
- data/lib/bio-ucsc/dp3/mrna.rb +11 -8
- data/lib/bio-ucsc/dp3/rmsk.rb +10 -7
- data/lib/bio-ucsc/droana2.rb +6 -4
- data/lib/bio-ucsc/droere1.rb +6 -4
- data/lib/bio-ucsc/drogri1.rb +6 -4
- data/lib/bio-ucsc/dromoj2.rb +7 -5
- data/lib/bio-ucsc/droper1.rb +7 -5
- data/lib/bio-ucsc/drosec1.rb +6 -4
- data/lib/bio-ucsc/drosim1.rb +6 -4
- data/lib/bio-ucsc/drosim1/chaindm3.rb +11 -8
- data/lib/bio-ucsc/drosim1/chaindm3link.rb +11 -8
- data/lib/bio-ucsc/drosim1/est.rb +11 -8
- data/lib/bio-ucsc/drosim1/gap.rb +11 -8
- data/lib/bio-ucsc/drosim1/gold.rb +11 -8
- data/lib/bio-ucsc/drosim1/intronest.rb +11 -8
- data/lib/bio-ucsc/drosim1/mrna.rb +11 -8
- data/lib/bio-ucsc/drosim1/rmsk.rb +10 -7
- data/lib/bio-ucsc/drovir2.rb +6 -4
- data/lib/bio-ucsc/droyak2.rb +6 -4
- data/lib/bio-ucsc/droyak2/chaindm3.rb +11 -8
- data/lib/bio-ucsc/droyak2/chaindm3link.rb +11 -8
- data/lib/bio-ucsc/droyak2/est.rb +11 -8
- data/lib/bio-ucsc/droyak2/gap.rb +11 -8
- data/lib/bio-ucsc/droyak2/gold.rb +11 -8
- data/lib/bio-ucsc/droyak2/intronest.rb +11 -8
- data/lib/bio-ucsc/droyak2/mrna.rb +11 -8
- data/lib/bio-ucsc/droyak2/rmsk.rb +10 -7
- data/lib/bio-ucsc/equcab2.rb +7 -4
- data/lib/bio-ucsc/equcab2/est.rb +11 -8
- data/lib/bio-ucsc/equcab2/gap.rb +11 -8
- data/lib/bio-ucsc/equcab2/gold.rb +11 -8
- data/lib/bio-ucsc/equcab2/intronest.rb +11 -8
- data/lib/bio-ucsc/equcab2/mrna.rb +11 -8
- data/lib/bio-ucsc/equcab2/rmsk.rb +10 -7
- data/lib/bio-ucsc/felcat4.rb +7 -4
- data/lib/bio-ucsc/file.rb +10 -0
- data/lib/bio-ucsc/file/bytequeue.rb +28 -0
- data/lib/bio-ucsc/file/twobit.rb +174 -0
- data/lib/bio-ucsc/fr2.rb +5 -3
- data/lib/bio-ucsc/fr2/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/fr2/chaingalgal3link.rb +11 -8
- data/lib/bio-ucsc/fr2/chaingasacu1.rb +11 -8
- data/lib/bio-ucsc/fr2/chaingasacu1link.rb +11 -8
- data/lib/bio-ucsc/fr2/chainmm9.rb +11 -8
- data/lib/bio-ucsc/fr2/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/fr2/chainorylat2.rb +11 -8
- data/lib/bio-ucsc/fr2/chainorylat2link.rb +11 -8
- data/lib/bio-ucsc/fr2/est.rb +11 -8
- data/lib/bio-ucsc/fr2/gap.rb +11 -8
- data/lib/bio-ucsc/fr2/gold.rb +11 -8
- data/lib/bio-ucsc/fr2/intronest.rb +11 -8
- data/lib/bio-ucsc/fr2/mrna.rb +11 -8
- data/lib/bio-ucsc/fr2/rmsk.rb +10 -7
- data/lib/bio-ucsc/galgal3.rb +8 -5
- data/lib/bio-ucsc/galgal3/chainanocar1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainanocar1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainbraflo1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainbraflo1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaincavpor3.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaincavpor3link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaindanrer4.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaindanrer4link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainfr2.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainfr2link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaingasacu1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaingasacu1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainmm9.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainornana1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainornana1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainpetmar1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainpetmar1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainrn4.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainrn4link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaintaegut1.rb +11 -8
- data/lib/bio-ucsc/galgal3/chaintaegut1link.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainxentro2.rb +11 -8
- data/lib/bio-ucsc/galgal3/chainxentro2link.rb +11 -8
- data/lib/bio-ucsc/galgal3/est.rb +11 -8
- data/lib/bio-ucsc/galgal3/gap.rb +11 -8
- data/lib/bio-ucsc/galgal3/gold.rb +11 -8
- data/lib/bio-ucsc/galgal3/intronest.rb +11 -8
- data/lib/bio-ucsc/galgal3/mrna.rb +11 -8
- data/lib/bio-ucsc/galgal3/rmsk.rb +10 -7
- data/lib/bio-ucsc/gasacu1.rb +6 -4
- data/lib/bio-ucsc/gasacu1/chainanocar1.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainanocar1link.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainfr2.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainfr2link.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chaingalgal3link.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainmm9.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainorylat2.rb +11 -8
- data/lib/bio-ucsc/gasacu1/chainorylat2link.rb +11 -8
- data/lib/bio-ucsc/gasacu1/est.rb +11 -8
- data/lib/bio-ucsc/gasacu1/intronest.rb +11 -8
- data/lib/bio-ucsc/gasacu1/mrna.rb +11 -8
- data/lib/bio-ucsc/gasacu1/rmsk.rb +10 -7
- data/lib/bio-ucsc/gi.rb +27 -0
- data/lib/bio-ucsc/go.rb +7 -4
- data/lib/bio-ucsc/hg18.rb +7 -4
- data/lib/bio-ucsc/hg18/chainanocar1.rb +11 -8
- data/lib/bio-ucsc/hg18/chainbostau4.rb +11 -8
- data/lib/bio-ucsc/hg18/chainbraflo1.rb +11 -8
- data/lib/bio-ucsc/hg18/chaincaljac1.rb +11 -8
- data/lib/bio-ucsc/hg18/chaincanfam2.rb +11 -8
- data/lib/bio-ucsc/hg18/chaincavpor3.rb +11 -8
- data/lib/bio-ucsc/hg18/chaindanrer5.rb +11 -8
- data/lib/bio-ucsc/hg18/chainequcab1.rb +11 -8
- data/lib/bio-ucsc/hg18/chainfelcat3.rb +11 -8
- data/lib/bio-ucsc/hg18/chainfr2.rb +12 -9
- data/lib/bio-ucsc/hg18/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/hg18/chaingasacu1.rb +11 -8
- data/lib/bio-ucsc/hg18/chainmm9.rb +11 -8
- data/lib/bio-ucsc/hg18/chainmondom4.rb +11 -8
- data/lib/bio-ucsc/hg18/chainornana1.rb +11 -8
- data/lib/bio-ucsc/hg18/chainorylat2.rb +11 -8
- data/lib/bio-ucsc/hg18/chainpantro2.rb +11 -8
- data/lib/bio-ucsc/hg18/chainpetmar1.rb +11 -8
- data/lib/bio-ucsc/hg18/chainponabe2.rb +11 -8
- data/lib/bio-ucsc/hg18/chainrhemac2.rb +11 -8
- data/lib/bio-ucsc/hg18/chainrn4.rb +11 -8
- data/lib/bio-ucsc/hg18/chainself.rb +11 -8
- data/lib/bio-ucsc/hg18/chainstrpur2.rb +11 -8
- data/lib/bio-ucsc/hg18/chaintaegut1.rb +11 -8
- data/lib/bio-ucsc/hg18/chaintetnig2.rb +11 -8
- data/lib/bio-ucsc/hg18/chainxentro2.rb +11 -8
- data/lib/bio-ucsc/hg18/gap.rb +11 -8
- data/lib/bio-ucsc/hg18/gold.rb +11 -8
- data/lib/bio-ucsc/hg18/intronest.rb +11 -8
- data/lib/bio-ucsc/hg18/rmsk.rb +10 -7
- data/lib/bio-ucsc/hg18/rmskrm327.rb +10 -7
- data/lib/bio-ucsc/hg19.rb +7 -6
- data/lib/bio-ucsc/hg19/description.rb +1 -1
- data/lib/bio-ucsc/hg19/gbcdnainfo.rb +2 -2
- data/lib/bio-ucsc/hgfixed.rb +7 -4
- data/lib/bio-ucsc/loxafr3.rb +7 -4
- data/lib/bio-ucsc/mm9.rb +7 -12
- data/lib/bio-ucsc/mm9/chainbraflo1.rb +11 -8
- data/lib/bio-ucsc/mm9/chainbraflo1link.rb +11 -8
- data/lib/bio-ucsc/mm9/chaincanfam2.rb +11 -8
- data/lib/bio-ucsc/mm9/chaincanfam2link.rb +11 -8
- data/lib/bio-ucsc/mm9/chaincavpor3.rb +11 -8
- data/lib/bio-ucsc/mm9/chaincavpor3link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainfr2.rb +11 -8
- data/lib/bio-ucsc/mm9/chainfr2link.rb +11 -8
- data/lib/bio-ucsc/mm9/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/mm9/chaingalgal3link.rb +11 -8
- data/lib/bio-ucsc/mm9/chaingasacu1.rb +11 -8
- data/lib/bio-ucsc/mm9/chaingasacu1link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainornana1.rb +11 -8
- data/lib/bio-ucsc/mm9/chainornana1link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainorylat2.rb +11 -8
- data/lib/bio-ucsc/mm9/chainorylat2link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainpetmar1.rb +11 -8
- data/lib/bio-ucsc/mm9/chainpetmar1link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainponabe2.rb +11 -8
- data/lib/bio-ucsc/mm9/chainponabe2link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainrhemac2.rb +11 -8
- data/lib/bio-ucsc/mm9/chainrhemac2link.rb +11 -8
- data/lib/bio-ucsc/mm9/chainrn4.rb +11 -8
- data/lib/bio-ucsc/mm9/chainrn4link.rb +11 -8
- data/lib/bio-ucsc/mm9/est.rb +11 -8
- data/lib/bio-ucsc/mm9/gap.rb +11 -8
- data/lib/bio-ucsc/mm9/gold.rb +11 -8
- data/lib/bio-ucsc/mm9/intronest.rb +11 -8
- data/lib/bio-ucsc/mm9/mrna.rb +11 -8
- data/lib/bio-ucsc/mm9/rmsk.rb +10 -7
- data/lib/bio-ucsc/mondom5.rb +7 -4
- data/lib/bio-ucsc/ornana1.rb +6 -3
- data/lib/bio-ucsc/orycun2.rb +5 -3
- data/lib/bio-ucsc/orylat2.rb +7 -5
- data/lib/bio-ucsc/oviari1.rb +6 -4
- data/lib/bio-ucsc/pantro3.rb +7 -5
- data/lib/bio-ucsc/petmar1.rb +6 -5
- data/lib/bio-ucsc/ponabe2.rb +6 -4
- data/lib/bio-ucsc/ponabe2/chainmm9.rb +11 -8
- data/lib/bio-ucsc/ponabe2/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/ponabe2/chainornana1.rb +11 -8
- data/lib/bio-ucsc/ponabe2/chainornana1link.rb +11 -8
- data/lib/bio-ucsc/ponabe2/chainrhemac2.rb +11 -8
- data/lib/bio-ucsc/ponabe2/chainrhemac2link.rb +11 -8
- data/lib/bio-ucsc/ponabe2/est.rb +11 -8
- data/lib/bio-ucsc/ponabe2/gap.rb +11 -8
- data/lib/bio-ucsc/ponabe2/gold.rb +11 -8
- data/lib/bio-ucsc/ponabe2/intronest.rb +11 -8
- data/lib/bio-ucsc/ponabe2/mrna.rb +11 -8
- data/lib/bio-ucsc/ponabe2/rmsk.rb +10 -7
- data/lib/bio-ucsc/pripac1.rb +7 -5
- data/lib/bio-ucsc/pripac1/chaincaepb1.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaincaepb1link.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaincaerem2.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaincaerem2link.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaincb3.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaincb3link.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaince6.rb +11 -8
- data/lib/bio-ucsc/pripac1/chaince6link.rb +11 -8
- data/lib/bio-ucsc/pripac1/gap.rb +11 -8
- data/lib/bio-ucsc/pripac1/gold.rb +11 -8
- data/lib/bio-ucsc/pripac1/rmsk.rb +10 -7
- data/lib/bio-ucsc/proteome.rb +7 -4
- data/lib/bio-ucsc/reference.rb +5 -160
- data/lib/bio-ucsc/rhemac2.rb +5 -5
- data/lib/bio-ucsc/rhemac2/chainmm9.rb +11 -8
- data/lib/bio-ucsc/rhemac2/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/rhemac2/chainponabe2.rb +11 -8
- data/lib/bio-ucsc/rhemac2/chainponabe2link.rb +11 -8
- data/lib/bio-ucsc/rhemac2/chainrn4.rb +11 -8
- data/lib/bio-ucsc/rhemac2/chainrn4link.rb +11 -8
- data/lib/bio-ucsc/rn4.rb +6 -8
- data/lib/bio-ucsc/rn4/chaincanfam2.rb +11 -8
- data/lib/bio-ucsc/rn4/chaincanfam2link.rb +11 -8
- data/lib/bio-ucsc/rn4/chaincavpor3.rb +11 -8
- data/lib/bio-ucsc/rn4/chaincavpor3link.rb +11 -8
- data/lib/bio-ucsc/rn4/chaindanrer4.rb +11 -8
- data/lib/bio-ucsc/rn4/chaindanrer4link.rb +11 -8
- data/lib/bio-ucsc/rn4/chainequcab1.rb +11 -8
- data/lib/bio-ucsc/rn4/chainequcab1link.rb +11 -8
- data/lib/bio-ucsc/rn4/chaingalgal3.rb +11 -8
- data/lib/bio-ucsc/rn4/chaingalgal3link.rb +11 -8
- data/lib/bio-ucsc/rn4/chainmm9.rb +11 -8
- data/lib/bio-ucsc/rn4/chainmm9link.rb +11 -8
- data/lib/bio-ucsc/rn4/chainmondom4.rb +11 -8
- data/lib/bio-ucsc/rn4/chainmondom4link.rb +11 -8
- data/lib/bio-ucsc/rn4/chainpantro2.rb +11 -8
- data/lib/bio-ucsc/rn4/chainpantro2link.rb +11 -8
- data/lib/bio-ucsc/rn4/chainrhemac2.rb +11 -8
- data/lib/bio-ucsc/rn4/chainrhemac2link.rb +11 -8
- data/lib/bio-ucsc/rn4/est.rb +11 -8
- data/lib/bio-ucsc/rn4/gap.rb +11 -8
- data/lib/bio-ucsc/rn4/gold.rb +11 -8
- data/lib/bio-ucsc/rn4/intronest.rb +11 -8
- data/lib/bio-ucsc/rn4/mrna.rb +11 -8
- data/lib/bio-ucsc/rn4/rmsk.rb +10 -7
- data/lib/bio-ucsc/saccer2.rb +6 -4
- data/lib/bio-ucsc/saccer2/est.rb +11 -8
- data/lib/bio-ucsc/saccer2/gap.rb +11 -8
- data/lib/bio-ucsc/saccer2/gold.rb +11 -8
- data/lib/bio-ucsc/saccer2/intronest.rb +11 -8
- data/lib/bio-ucsc/saccer2/mrna.rb +11 -8
- data/lib/bio-ucsc/saccer2/t2micron_est.rb +4 -4
- data/lib/bio-ucsc/saccer2/t2micron_gap.rb +4 -4
- data/lib/bio-ucsc/saccer2/t2micron_gold.rb +4 -4
- data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb +4 -4
- data/lib/bio-ucsc/saccer2/t2micron_mrna.rb +4 -4
- data/lib/bio-ucsc/strpur2.rb +7 -15
- data/lib/bio-ucsc/susscr2.rb +6 -4
- data/lib/bio-ucsc/susscr2/est.rb +11 -8
- data/lib/bio-ucsc/susscr2/intronest.rb +11 -8
- data/lib/bio-ucsc/susscr2/mrna.rb +11 -8
- data/lib/bio-ucsc/table_class_detector.rb +250 -475
- data/lib/bio-ucsc/taegut1.rb +6 -4
- data/lib/bio-ucsc/taegut1/chaingalgal3.rb +14 -13
- data/lib/bio-ucsc/taegut1/chaingalgal3link.rb +13 -10
- data/lib/bio-ucsc/taegut1/est.rb +13 -10
- data/lib/bio-ucsc/taegut1/gap.rb +13 -10
- data/lib/bio-ucsc/taegut1/gold.rb +13 -10
- data/lib/bio-ucsc/taegut1/intronest.rb +13 -10
- data/lib/bio-ucsc/taegut1/mrna.rb +13 -10
- data/lib/bio-ucsc/taegut1/rmsk.rb +12 -9
- data/lib/bio-ucsc/tetnig2.rb +6 -4
- data/lib/bio-ucsc/tetnig2/mrna.rb +11 -8
- data/lib/bio-ucsc/uniprot.rb +7 -4
- data/lib/bio-ucsc/visigene.rb +6 -3
- data/lib/bio-ucsc/xentro2.rb +6 -12
- data/samples/num-gene-exon.rb +1 -2
- data/samples/snp2genes.rb +1 -7
- data/samples/symbol2summary.rb +7 -1
- data/spec/ailmel1_spec.rb +245 -245
- data/spec/aplcal1_spec.rb +0 -30
- data/spec/braflo1_spec.rb +1 -1
- data/spec/canfam2_spec.rb +6 -6
- data/spec/danrer7_spec.rb +6 -6
- data/spec/file/twobit.rb +167 -0
- data/spec/galgal3_spec.rb +12 -12
- data/spec/gasacu1_spec.rb +6 -6
- data/spec/hg18/find_by_spec.rb +14 -20
- data/spec/hg19/all_mrna_spec.rb +0 -8
- data/spec/hg19/altseqliftoverpsl_spec.rb +0 -8
- data/spec/hg19/altseqpatches_spec.rb +0 -8
- data/spec/hg19/{chainanocar1_spec.rb → chainanocar2_spec.rb} +2 -2
- data/spec/hg19/{chainbostau4_spec.rb → chainbostau6_spec.rb} +2 -2
- data/spec/hg19/{chainxentro2_spec.rb → chainxentro3_spec.rb} +2 -2
- data/spec/hg19/connect_spec.rb +20 -0
- data/spec/hg19/find_by_spec.rb +14 -14
- data/spec/hg19/gwascatalog_spec.rb +0 -7
- data/spec/hg19/hgikmcextra_spec.rb +2 -1
- data/spec/hg19/mrnaorinetinfo_spec.rb +0 -8
- data/spec/hg19/{netanocar1_spec.rb → netanocar2_spec.rb} +2 -2
- data/spec/hg19/{netbostau4_spec.rb → netbostau6_spec.rb} +2 -2
- data/spec/hg19/{netxentro2_spec.rb → netxentro3_spec.rb} +2 -2
- data/spec/hg19/sibtxgraph_spec.rb +0 -8
- data/spec/hg19/snp132_spec.rb +9 -0
- data/spec/hg19/xenorefflat_spec.rb +0 -8
- data/spec/hg19/xenorefgene_spec.rb +0 -8
- data/spec/hg19/xenorefseqali_spec.rb +0 -8
- data/spec/mm9_spec.rb +32 -32
- data/spec/ornana1_spec.rb +12 -12
- data/spec/{named_scope_spec.rb → relation_objects_spec.rb} +14 -0
- data/spec/rhemac2_spec.rb +16 -6
- data/spec/rn4_spec.rb +12 -12
- data/spec/spec_helper.rb +3 -1
- data/spec/susscr2_spec.rb +6 -6
- data/spec/taegut1_spec.rb +8 -8
- data/spec/xentro2_spec.rb +6 -6
- metadata +63 -138
- data/README.rdoc +0 -202
- data/lib/bio-ucsc/ailmel1/db_connection.rb +0 -57
- data/lib/bio-ucsc/anocar2/db_connection.rb +0 -57
- data/lib/bio-ucsc/anogam1/db_connection.rb +0 -57
- data/lib/bio-ucsc/aplcal1/db_connection.rb +0 -57
- data/lib/bio-ucsc/bostau4/db_connection.rb +0 -57
- data/lib/bio-ucsc/braflo1/db_connection.rb +0 -57
- data/lib/bio-ucsc/caejap1/db_connection.rb +0 -57
- data/lib/bio-ucsc/caepb2/db_connection.rb +0 -57
- data/lib/bio-ucsc/caerem3/db_connection.rb +0 -57
- data/lib/bio-ucsc/caljac3/db_connection.rb +0 -55
- data/lib/bio-ucsc/canfam2/db_connection.rb +0 -57
- data/lib/bio-ucsc/cavpor3/db_connection.rb +0 -57
- data/lib/bio-ucsc/cb3/db_connection.rb +0 -57
- data/lib/bio-ucsc/ce6/db_connection.rb +0 -55
- data/lib/bio-ucsc/ci2/db_connection.rb +0 -55
- data/lib/bio-ucsc/danrer7/db_connection.rb +0 -57
- data/lib/bio-ucsc/dm3/db_connection.rb +0 -55
- data/lib/bio-ucsc/dp3/db_connection.rb +0 -57
- data/lib/bio-ucsc/droana2/db_connection.rb +0 -57
- data/lib/bio-ucsc/droere1/db_connection.rb +0 -57
- data/lib/bio-ucsc/drogri1/db_connection.rb +0 -57
- data/lib/bio-ucsc/dromoj2/db_connection.rb +0 -57
- data/lib/bio-ucsc/droper1/db_connection.rb +0 -57
- data/lib/bio-ucsc/drosec1/db_connection.rb +0 -57
- data/lib/bio-ucsc/drosim1/db_connection.rb +0 -57
- data/lib/bio-ucsc/drovir2/db_connection.rb +0 -57
- data/lib/bio-ucsc/droyak2/db_connection.rb +0 -57
- data/lib/bio-ucsc/equcab2/db_connection.rb +0 -57
- data/lib/bio-ucsc/felcat4/db_connection.rb +0 -57
- data/lib/bio-ucsc/fr2/db_connection.rb +0 -57
- data/lib/bio-ucsc/galgal3/db_connection.rb +0 -57
- data/lib/bio-ucsc/gasacu1/db_connection.rb +0 -57
- data/lib/bio-ucsc/go/db_connection.rb +0 -55
- data/lib/bio-ucsc/hg18/db_connection.rb +0 -59
- data/lib/bio-ucsc/hg19/db_connection.rb +0 -61
- data/lib/bio-ucsc/hgfixed/db_connection.rb +0 -55
- data/lib/bio-ucsc/loxafr3/db_connection.rb +0 -57
- data/lib/bio-ucsc/mm9/chainanocar1.rb +0 -79
- data/lib/bio-ucsc/mm9/chainanocar1link.rb +0 -79
- data/lib/bio-ucsc/mm9/chainbostau4.rb +0 -79
- data/lib/bio-ucsc/mm9/chainbostau4link.rb +0 -79
- data/lib/bio-ucsc/mm9/chainpantro2.rb +0 -81
- data/lib/bio-ucsc/mm9/chainpantro2link.rb +0 -82
- data/lib/bio-ucsc/mm9/chainxentro2.rb +0 -81
- data/lib/bio-ucsc/mm9/chainxentro2link.rb +0 -81
- data/lib/bio-ucsc/mm9/db_connection.rb +0 -55
- data/lib/bio-ucsc/mondom5/db_connection.rb +0 -57
- data/lib/bio-ucsc/ornana1/db_connection.rb +0 -57
- data/lib/bio-ucsc/orycun2/db_connection.rb +0 -57
- data/lib/bio-ucsc/orylat2/db_connection.rb +0 -55
- data/lib/bio-ucsc/oviari1/db_connection.rb +0 -57
- data/lib/bio-ucsc/pantro3/db_connection.rb +0 -55
- data/lib/bio-ucsc/petmar1/db_connection.rb +0 -57
- data/lib/bio-ucsc/ponabe2/db_connection.rb +0 -55
- data/lib/bio-ucsc/pripac1/db_connection.rb +0 -57
- data/lib/bio-ucsc/proteome/db_connection.rb +0 -59
- data/lib/bio-ucsc/rhemac2/chainpantro2.rb +0 -81
- data/lib/bio-ucsc/rhemac2/chainpantro2link.rb +0 -81
- data/lib/bio-ucsc/rhemac2/db_connection.rb +0 -55
- data/lib/bio-ucsc/rn4/chainbostau3.rb +0 -79
- data/lib/bio-ucsc/rn4/chainbostau3link.rb +0 -79
- data/lib/bio-ucsc/rn4/chainxentro2.rb +0 -81
- data/lib/bio-ucsc/rn4/chainxentro2link.rb +0 -81
- data/lib/bio-ucsc/rn4/db_connection.rb +0 -55
- data/lib/bio-ucsc/saccer2/db_connection.rb +0 -55
- data/lib/bio-ucsc/strpur2/chaingalgal3.rb +0 -81
- data/lib/bio-ucsc/strpur2/chaingalgal3link.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainhg18.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainhg18link.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainmm9.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainmm9link.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainpetmar1.rb +0 -81
- data/lib/bio-ucsc/strpur2/chainpetmar1link.rb +0 -81
- data/lib/bio-ucsc/strpur2/db_connection.rb +0 -57
- data/lib/bio-ucsc/strpur2/gap.rb +0 -81
- data/lib/bio-ucsc/strpur2/gold.rb +0 -81
- data/lib/bio-ucsc/susscr2/db_connection.rb +0 -57
- data/lib/bio-ucsc/taegut1/db_connection.rb +0 -57
- data/lib/bio-ucsc/tetnig2/db_connection.rb +0 -57
- data/lib/bio-ucsc/uniprot/db_connection.rb +0 -59
- data/lib/bio-ucsc/visigene/db_connection.rb +0 -55
- data/lib/bio-ucsc/xentro2/chaingalgal3.rb +0 -81
- data/lib/bio-ucsc/xentro2/chaingalgal3link.rb +0 -81
- data/lib/bio-ucsc/xentro2/db_connection.rb +0 -57
- data/lib/bio-ucsc/xentro2/est.rb +0 -81
- data/lib/bio-ucsc/xentro2/gap.rb +0 -81
- data/lib/bio-ucsc/xentro2/gold.rb +0 -81
- data/lib/bio-ucsc/xentro2/intronest.rb +0 -81
- data/lib/bio-ucsc/xentro2/mrna.rb +0 -81
- data/lib/bio-ucsc/xentro2/rmsk.rb +0 -78
- data/spec/hg19/chainaplcal1_spec.rb +0 -16
- data/spec/hg19/netaplcal1_spec.rb +0 -16
@@ -13,21 +13,24 @@ module Bio
|
|
13
13
|
module PriPac1
|
14
14
|
|
15
15
|
class Rmsk
|
16
|
+
include DBConnector
|
17
|
+
DBConnection.database "priPac1"
|
18
|
+
|
16
19
|
Bio::Ucsc::PriPac1::CHROMS.each do |chr|
|
17
20
|
class_eval %!
|
18
21
|
class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
|
19
|
-
|
20
|
-
|
22
|
+
self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
|
23
|
+
self.primary_key = nil
|
21
24
|
|
22
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
25
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
23
26
|
find_first_or_all_by_interval(interval, :first, opt)
|
24
27
|
end
|
25
28
|
|
26
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
29
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
27
30
|
find_first_or_all_by_interval(interval, :all, opt)
|
28
31
|
end
|
29
32
|
|
30
|
-
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
33
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt); interval = Bio::Ucsc::Gi.wrap(interval)
|
31
34
|
zstart = interval.zero_start
|
32
35
|
zend = interval.zero_end
|
33
36
|
if opt[:partial] == true
|
@@ -60,13 +63,13 @@ AND (genoEnd BETWEEN :zstart AND :zend))
|
|
60
63
|
!
|
61
64
|
end # each chromosome
|
62
65
|
|
63
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
66
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
64
67
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
65
68
|
chr_klass = self.const_get("#{chrom}_Rmsk")
|
66
69
|
chr_klass.__send__(:find_by_interval, interval, opt)
|
67
70
|
end
|
68
71
|
|
69
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
72
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
70
73
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
71
74
|
chr_klass = self.const_get("#{chrom}_Rmsk")
|
72
75
|
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
data/lib/bio-ucsc/proteome.rb
CHANGED
@@ -1,19 +1,22 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of Proteome
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011, 2012
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
6
|
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
7
7
|
#
|
8
8
|
|
9
|
-
require "#{File.dirname(__FILE__)}/
|
10
|
-
require "#{File.dirname(__FILE__)}/table_class_detector"
|
9
|
+
require "#{::File.dirname(__FILE__)}/db_connector"
|
10
|
+
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
11
11
|
|
12
12
|
module Bio
|
13
13
|
module Ucsc
|
14
14
|
module Proteome
|
15
15
|
extend TableClassDetector
|
16
|
-
|
16
|
+
include DBConnector
|
17
|
+
DBConnection.database "proteome"
|
18
|
+
|
19
|
+
base = "#{::File.dirname(__FILE__)}/proteome"
|
17
20
|
end
|
18
21
|
end
|
19
22
|
end
|
data/lib/bio-ucsc/reference.rb
CHANGED
@@ -1,6 +1,7 @@
|
|
1
1
|
#
|
2
2
|
# = reference.rb
|
3
3
|
# handle UCSC's 2bit file (locally stored) to retrieve the reference sequence
|
4
|
+
# after ver.0.4.0, Bio::Ucsc::Reference is moved to Bio::Ucsc::File::Twobit
|
4
5
|
#
|
5
6
|
# Copyright:: Cioyrught (C) 2011
|
6
7
|
# MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
@@ -8,168 +9,12 @@
|
|
8
9
|
|
9
10
|
module Bio
|
10
11
|
module Ucsc
|
11
|
-
TwoBitHeader =
|
12
|
-
|
13
|
-
TwoBitRecord =
|
14
|
-
Struct.new(:dna_size,
|
15
|
-
:n_block_intervals, :mask_block_intervals,
|
16
|
-
:reserved, :packed_dna_offset)
|
12
|
+
TwoBitHeader = File::Twobit::TwoBitHeader
|
13
|
+
TwoBitRecord = File::Twobit::TwoBitRecord
|
17
14
|
|
18
|
-
class ByteQueue
|
19
|
-
def initialize(str)
|
20
|
-
@str = str
|
21
|
-
@index = 0
|
22
|
-
end
|
15
|
+
class ByteQueue < File::ByteQueue; end
|
23
16
|
|
24
|
-
|
25
|
-
|
26
|
-
def next(n)
|
27
|
-
result = @str[@index, n]
|
28
|
-
@index += n
|
29
|
-
result
|
30
|
-
end
|
31
|
-
end # class ByteQueue
|
17
|
+
class Reference < File::Twobit; end
|
32
18
|
|
33
|
-
class Reference
|
34
|
-
BINCODE = {0b00 => "T", 0b01 => "C", 0b10 => "A", 0b11 => "G"}
|
35
|
-
|
36
|
-
def initialize(twobit_queue, filename, header, offsets)
|
37
|
-
@tbq = twobit_queue
|
38
|
-
@filename = filename
|
39
|
-
@header = header
|
40
|
-
@offsets = offsets
|
41
|
-
@records = Hash.new
|
42
|
-
end
|
43
|
-
|
44
|
-
attr_reader :filename, :header, :offsets
|
45
|
-
|
46
|
-
def self.load(filename)
|
47
|
-
two_bit = nil
|
48
|
-
open(filename, 'rb') {|f| two_bit = f.read}
|
49
|
-
tbq = ByteQueue.new(two_bit)
|
50
|
-
|
51
|
-
twobit_header = TwoBitHeader.new
|
52
|
-
twobit_header.signature = tbq.next(4).unpack('L').first
|
53
|
-
twobit_header.version = tbq.next(4).unpack('L').first
|
54
|
-
twobit_header.sequence_count = tbq.next(4).unpack('L').first
|
55
|
-
twobit_header.reserved = tbq.next(4).unpack('L').first
|
56
|
-
|
57
|
-
offsets = Hash.new
|
58
|
-
twobit_header.sequence_count.times do
|
59
|
-
name_length = tbq.next(1).unpack('C').first
|
60
|
-
offsets[tbq.next(name_length).unpack('a*').first] =
|
61
|
-
tbq.next(4).unpack('L').first
|
62
|
-
end
|
63
|
-
|
64
|
-
new(tbq, filename, twobit_header, offsets)
|
65
|
-
end
|
66
|
-
|
67
|
-
def records(chrom)
|
68
|
-
return @records[chrom] if @records[chrom]
|
69
|
-
|
70
|
-
@tbq.index = @offsets[chrom]
|
71
|
-
@records[chrom] = TwoBitRecord.new
|
72
|
-
@records[chrom].dna_size = @tbq.next(4).unpack('L').first
|
73
|
-
|
74
|
-
n_block_count = @tbq.next(4).unpack('L').first
|
75
|
-
n_block_starts = Array.new
|
76
|
-
n_block_count.times do
|
77
|
-
n_block_starts << @tbq.next(4).unpack('L').first
|
78
|
-
end
|
79
|
-
n_block_sizes = Array.new
|
80
|
-
n_block_count.times do
|
81
|
-
n_block_sizes << @tbq.next(4).unpack('L').first
|
82
|
-
end
|
83
|
-
@records[chrom].n_block_intervals = Array.new
|
84
|
-
n_block_count.times do |idx|
|
85
|
-
@records[chrom].n_block_intervals <<
|
86
|
-
Bio::GenomicInterval.zero_based(chrom,
|
87
|
-
n_block_starts[idx],
|
88
|
-
n_block_starts[idx]+n_block_sizes[idx])
|
89
|
-
end
|
90
|
-
|
91
|
-
mask_block_count = @tbq.next(4).unpack('L').first
|
92
|
-
mask_block_starts = Array.new
|
93
|
-
mask_block_count.times do
|
94
|
-
mask_block_starts << @tbq.next(4).unpack('L').first
|
95
|
-
end
|
96
|
-
mask_block_sizes = Array.new
|
97
|
-
mask_block_count.times do
|
98
|
-
mask_block_sizes << @tbq.next(4).unpack('L').first
|
99
|
-
end
|
100
|
-
@records[chrom].mask_block_intervals = Array.new
|
101
|
-
mask_block_count.times do |idx|
|
102
|
-
@records[chrom].mask_block_intervals <<
|
103
|
-
Bio::GenomicInterval.zero_based(chrom,
|
104
|
-
mask_block_starts[idx],
|
105
|
-
mask_block_starts[idx]+mask_block_sizes[idx])
|
106
|
-
end
|
107
|
-
|
108
|
-
@records[chrom].reserved = @tbq.next(4).unpack('L').first
|
109
|
-
@records[chrom].packed_dna_offset = @tbq.index
|
110
|
-
|
111
|
-
@records[chrom]
|
112
|
-
end
|
113
|
-
|
114
|
-
def find_by_interval(interval)
|
115
|
-
seq = self.find_by_interval_raw(interval)
|
116
|
-
@records[interval.chrom].n_block_intervals.map do |nb|
|
117
|
-
if interval.overlapped?(nb)
|
118
|
-
case interval.compare(nb)
|
119
|
-
when :equal,:contained_by
|
120
|
-
seq = 'N' * interval.overlap(nb)
|
121
|
-
when :contains
|
122
|
-
left_len = nb.chr_start - interval.chr_start + 1
|
123
|
-
right_len = interval.chr_end - nb.chr_end + 1
|
124
|
-
seq[0, left_len] = 'N' * left_len
|
125
|
-
seq[-right_len, right_len] = 'N' * right_len
|
126
|
-
when :left_overlapped
|
127
|
-
left_len = nb.chr_end - interval.chr_start + 1
|
128
|
-
seq[0, left_len] = 'N' * left_len
|
129
|
-
when :right_overlapped
|
130
|
-
right_len = interval.chr_end - nb.chr_start + 1
|
131
|
-
seq[-right_len, right_len] = 'N' * right_len
|
132
|
-
when :right_adjacent, :right_off
|
133
|
-
# expecting that N-blocks are sorted
|
134
|
-
# return Bio::Sequence::NA.new(seq)
|
135
|
-
seq
|
136
|
-
end
|
137
|
-
end
|
138
|
-
end
|
139
|
-
#Bio::Sequence::NA.new(seq)
|
140
|
-
seq
|
141
|
-
end
|
142
|
-
|
143
|
-
def find_by_interval_raw(interval)
|
144
|
-
byte_count, byte_mod = interval.zero_start.divmod 4
|
145
|
-
chrom_top = self.records(interval.chrom).packed_dna_offset
|
146
|
-
div_start, mod_start = interval.zero_start.divmod 4
|
147
|
-
div_end, mod_end = interval.zero_end.divmod 4
|
148
|
-
div_len, mod_len = interval.length.divmod 4
|
149
|
-
|
150
|
-
byte_length = div_end - div_start + 1
|
151
|
-
@tbq.index = chrom_top + div_start
|
152
|
-
bytes = @tbq.next(byte_length).unpack('C*')
|
153
|
-
seq = bytes_to_nucleotides(bytes)
|
154
|
-
seq[mod_start..(-1-(4-mod_end))]
|
155
|
-
end
|
156
|
-
|
157
|
-
private
|
158
|
-
|
159
|
-
def bytes_to_nucleotides(bytes)
|
160
|
-
results = ""
|
161
|
-
bytes.each do |byte|
|
162
|
-
results << byte_to_nucleotides(byte)
|
163
|
-
end
|
164
|
-
results
|
165
|
-
end
|
166
|
-
|
167
|
-
def byte_to_nucleotides(byte)
|
168
|
-
BINCODE[byte >> 6] +
|
169
|
-
BINCODE[(byte >> 4) & 0b11] +
|
170
|
-
BINCODE[(byte >> 2) & 0b11] +
|
171
|
-
BINCODE[byte & 0b11]
|
172
|
-
end
|
173
|
-
end # class ReferenceSequence
|
174
19
|
end # module Ucsc
|
175
20
|
end # module Bio
|
data/lib/bio-ucsc/rhemac2.rb
CHANGED
@@ -6,8 +6,8 @@
|
|
6
6
|
# License:: The Ruby licence (Ryby's / GPLv2 dual)
|
7
7
|
#
|
8
8
|
|
9
|
-
require "#{File.dirname(__FILE__)}/
|
10
|
-
require "#{File.dirname(__FILE__)}/table_class_detector"
|
9
|
+
require "#{::File.dirname(__FILE__)}/db_connector"
|
10
|
+
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
11
11
|
|
12
12
|
module Bio
|
13
13
|
module Ucsc
|
@@ -17,12 +17,12 @@ module Bio
|
|
17
17
|
Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
|
18
18
|
Chr20 ChrX)
|
19
19
|
extend TableClassDetector
|
20
|
+
include DBConnector
|
21
|
+
DBConnection.database "rheMac2"
|
20
22
|
|
21
|
-
base = "#{File.dirname(__FILE__)}/rhemac2"
|
23
|
+
base = "#{::File.dirname(__FILE__)}/rhemac2"
|
22
24
|
autoload :ChainMm9, "#{base}/chainmm9"
|
23
25
|
autoload :ChainMm9Link, "#{base}/chainmm9link"
|
24
|
-
autoload :ChainPanTro2, "#{base}/chainpantro2"
|
25
|
-
autoload :ChainPanTro2Link, "#{base}/chainpantro2link"
|
26
26
|
autoload :ChainPonAbe2, "#{base}/chainponabe2"
|
27
27
|
autoload :ChainPonAbe2Link, "#{base}/chainponabe2link"
|
28
28
|
autoload :ChainRn4, "#{base}/chainrn4"
|
@@ -12,25 +12,28 @@ module Bio
|
|
12
12
|
module RheMac2
|
13
13
|
|
14
14
|
class ChainMm9
|
15
|
+
include DBConnector
|
16
|
+
DBConnection.database "rheMac2"
|
17
|
+
|
15
18
|
KLASS = "ChainMm9"
|
16
19
|
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
20
|
|
18
21
|
Bio::Ucsc::RheMac2::CHROMS.each do |chr|
|
19
22
|
class_eval %!
|
20
23
|
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
+
self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
25
|
+
self.primary_key = nil
|
26
|
+
self.inheritance_column = nil
|
24
27
|
|
25
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
28
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
26
29
|
find_first_or_all_by_interval(interval, :first, opt)
|
27
30
|
end
|
28
31
|
|
29
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
32
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
30
33
|
find_first_or_all_by_interval(interval, :all, opt)
|
31
34
|
end
|
32
35
|
|
33
|
-
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
36
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt); interval = Bio::Ucsc::Gi.wrap(interval)
|
34
37
|
zstart = interval.zero_start
|
35
38
|
zend = interval.zero_end
|
36
39
|
if opt[:partial] == true
|
@@ -63,13 +66,13 @@ AND (tEnd BETWEEN :zstart AND :zend))
|
|
63
66
|
!
|
64
67
|
end # each chromosome
|
65
68
|
|
66
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
69
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
67
70
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
71
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
72
|
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
73
|
end
|
71
74
|
|
72
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
75
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
73
76
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
77
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
78
|
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
@@ -12,25 +12,28 @@ module Bio
|
|
12
12
|
module RheMac2
|
13
13
|
|
14
14
|
class ChainMm9Link
|
15
|
+
include DBConnector
|
16
|
+
DBConnection.database "rheMac2"
|
17
|
+
|
15
18
|
KLASS = "ChainMm9Link"
|
16
19
|
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
20
|
|
18
21
|
Bio::Ucsc::RheMac2::CHROMS.each do |chr|
|
19
22
|
class_eval %!
|
20
23
|
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
+
self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
25
|
+
self.primary_key = nil
|
26
|
+
self.inheritance_column = nil
|
24
27
|
|
25
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
28
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
26
29
|
find_first_or_all_by_interval(interval, :first, opt)
|
27
30
|
end
|
28
31
|
|
29
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
32
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
30
33
|
find_first_or_all_by_interval(interval, :all, opt)
|
31
34
|
end
|
32
35
|
|
33
|
-
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
36
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt); interval = Bio::Ucsc::Gi.wrap(interval)
|
34
37
|
zstart = interval.zero_start
|
35
38
|
zend = interval.zero_end
|
36
39
|
if opt[:partial] == true
|
@@ -63,13 +66,13 @@ AND (tEnd BETWEEN :zstart AND :zend))
|
|
63
66
|
!
|
64
67
|
end # each chromosome
|
65
68
|
|
66
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
69
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
67
70
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
71
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
72
|
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
73
|
end
|
71
74
|
|
72
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
75
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
73
76
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
77
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
78
|
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
@@ -12,25 +12,28 @@ module Bio
|
|
12
12
|
module RheMac2
|
13
13
|
|
14
14
|
class ChainPonAbe2
|
15
|
+
include DBConnector
|
16
|
+
DBConnection.database "rheMac2"
|
17
|
+
|
15
18
|
KLASS = "ChainPonAbe2"
|
16
19
|
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
20
|
|
18
21
|
Bio::Ucsc::RheMac2::CHROMS.each do |chr|
|
19
22
|
class_eval %!
|
20
23
|
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
+
self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
25
|
+
self.primary_key = nil
|
26
|
+
self.inheritance_column = nil
|
24
27
|
|
25
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
28
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
26
29
|
find_first_or_all_by_interval(interval, :first, opt)
|
27
30
|
end
|
28
31
|
|
29
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
32
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
30
33
|
find_first_or_all_by_interval(interval, :all, opt)
|
31
34
|
end
|
32
35
|
|
33
|
-
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
36
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt); interval = Bio::Ucsc::Gi.wrap(interval)
|
34
37
|
zstart = interval.zero_start
|
35
38
|
zend = interval.zero_end
|
36
39
|
if opt[:partial] == true
|
@@ -63,13 +66,13 @@ AND (tEnd BETWEEN :zstart AND :zend))
|
|
63
66
|
!
|
64
67
|
end # each chromosome
|
65
68
|
|
66
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
69
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
67
70
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
71
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
72
|
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
73
|
end
|
71
74
|
|
72
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
75
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
73
76
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
77
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
78
|
chr_klass.__send__(:find_all_by_interval, interval, opt)
|
@@ -12,25 +12,28 @@ module Bio
|
|
12
12
|
module RheMac2
|
13
13
|
|
14
14
|
class ChainPonAbe2Link
|
15
|
+
include DBConnector
|
16
|
+
DBConnection.database "rheMac2"
|
17
|
+
|
15
18
|
KLASS = "ChainPonAbe2Link"
|
16
19
|
KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
|
17
20
|
|
18
21
|
Bio::Ucsc::RheMac2::CHROMS.each do |chr|
|
19
22
|
class_eval %!
|
20
23
|
class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
|
21
|
-
|
22
|
-
|
23
|
-
|
24
|
+
self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
|
25
|
+
self.primary_key = nil
|
26
|
+
self.inheritance_column = nil
|
24
27
|
|
25
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
28
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
26
29
|
find_first_or_all_by_interval(interval, :first, opt)
|
27
30
|
end
|
28
31
|
|
29
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
32
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
30
33
|
find_first_or_all_by_interval(interval, :all, opt)
|
31
34
|
end
|
32
35
|
|
33
|
-
def self.find_first_or_all_by_interval(interval, first_all, opt)
|
36
|
+
def self.find_first_or_all_by_interval(interval, first_all, opt); interval = Bio::Ucsc::Gi.wrap(interval)
|
34
37
|
zstart = interval.zero_start
|
35
38
|
zend = interval.zero_end
|
36
39
|
if opt[:partial] == true
|
@@ -63,13 +66,13 @@ AND (tEnd BETWEEN :zstart AND :zend))
|
|
63
66
|
!
|
64
67
|
end # each chromosome
|
65
68
|
|
66
|
-
def self.find_by_interval(interval, opt = {:partial => true})
|
69
|
+
def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
67
70
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
68
71
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
69
72
|
chr_klass.__send__(:find_by_interval, interval, opt)
|
70
73
|
end
|
71
74
|
|
72
|
-
def self.find_all_by_interval(interval, opt = {:partial => true})
|
75
|
+
def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
|
73
76
|
chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
|
74
77
|
chr_klass = self.const_get("#{chrom}_#{KLASS}")
|
75
78
|
chr_klass.__send__(:find_all_by_interval, interval, opt)
|