Mercurial > repos > jeremyjliu > region_motif_data_manager

comparison data_manager/data_manager_fetch_motifs.py @ 11:24a2c2783fb8 draft

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author jeremyjliu
date Tue, 07 Apr 2015 23:19:04 -0400
parents a5421f83f972
children 377723319b45
comparison
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10:a5421f83f972 11:24a2c2783fb8
26 if motif_db == "encode": 26 if motif_db == "encode":
27 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz', 27 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz',
28 "pouya_motifs.bed.bgz", "encode_bgz", "Encode Motifs (hg19) BGZ"] 28 "pouya_motifs.bed.bgz", "encode_bgz", "Encode Motifs (hg19) BGZ"]
29 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz.tbi', 29 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz.tbi',
30 "pouya_motifs.bed.bgz.tbi", "encode_tbi", "Encode Motifs (hg19) TBI"] 30 "pouya_motifs.bed.bgz.tbi", "encode_tbi", "Encode Motifs (hg19) TBI"]
31 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.RData', 31 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.meme.txt',
32 "pouya.pwms.from.seq.RData", "encode_pwm", "Encode Motifs (hg19) PWM"] 32 "pouya.pwms.from.seq.RData", "encode_pwm", "Encode Motifs (hg19) PWM MEME"]
33 elif motif_db == "jaspar": 33 elif motif_db == "jaspar":
34 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz', 34 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz',
35 "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"] 35 "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
36 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz.tbi', 36 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz.tbi',
37 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"] 37 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"]
38 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/jaspar.jolma.pwms.from.seq.RData', 38 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/jaspar.jolma.pwms.from.seq.meme.txt',
39 "jaspar.jolma.pwms.from.seq.RData", "jaspar_pwm", "Jaspar and Jolma Motifs (hg19) PWM"] 39 "jaspar.jolma.pwms.from.seq.RData", "jaspar_pwm", "Jaspar and Jolma Motifs (hg19) PWM MEME"]
40 elif motif_db == "mouse": 40 elif motif_db == "mouse":
41 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz', 41 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz',
42 "mm9_motifs_split.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"] 42 "mm9_motifs_split.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
43 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz.tbi', 43 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz.tbi',
44 "mm9_motifs_split.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"] 44 "mm9_motifs_split.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
45 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/mm9.pwms.from.seq.RData', 45 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/mm9.pwms.from.seq.meme.txt',
46 "mm9.pwms.from.seq.RData", "mouse_pwm", "Mouse Motifs (mm9) PWM"] 46 "mm9.pwms.from.seq.RData", "mouse_pwm", "Mouse Motifs (mm9) PWM MEME"]
47 else: 47 else:
48 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz', 48 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz',
49 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Encode Motifs (hg19) BGZ"] 49 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Encode Motifs (hg19) BGZ"]
50 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz.tbi', 50 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz.tbi',
51 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Encode Motifs (hg19) TBI"] 51 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Encode Motifs (hg19) TBI"]
52 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.RData', 52 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.meme.txt',
53 "pouya.pwms.from.seq.RData", "test_pwm", "Test Encode Motifs (hg19) PWM"] 53 "pouya.pwms.from.seq.RData", "test_pwm", "Test Encode Motifs (hg19) PWM MEME"]
54 54
55 55
56 # Save and add motif bgz file to motif_databases data table 56 # Save and add motif bgz file to motif_databases data table
57 bgz_reader = urllib2.urlopen( BGZ[0] ) 57 bgz_reader = urllib2.urlopen( BGZ[0] )
58 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params, 58 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,