Mercurial > repos > jeremyjliu > region_motif_data_manager
comparison data_manager/data_manager_fetch_motifs.py @ 12:377723319b45 draft default tip
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| author | jeremyjliu |
|---|---|
| date | Tue, 07 Apr 2015 23:53:02 -0400 |
| parents | 24a2c2783fb8 |
| children |
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| 11:24a2c2783fb8 | 12:377723319b45 |
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| 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.meme.txt', | 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 MEME"] | 32 "pouya.pwms.from.seq.meme.txt", "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.meme.txt', | 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 MEME"] | 39 "jaspar.jolma.pwms.from.seq.meme.txt", "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.meme.txt', | 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 MEME"] | 46 "mm9.pwms.from.seq.meme.txt", "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.meme.txt', | 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 MEME"] | 53 "pouya.pwms.from.seq.meme.txt", "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, |