[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Script that imports locally stored data as a new dataset for the user |
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| 5 | Usage: import id outputfile |
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| 6 | """ |
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| 7 | import sys, os |
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| 8 | |
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| 9 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 10 | |
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| 11 | BUFFER = 1048576 |
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| 12 | |
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| 13 | dataid = sys.argv[1] |
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| 14 | out_name = sys.argv[2] |
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| 15 | |
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| 16 | |
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| 17 | id2name = { |
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| 18 | 'eryth' : 'ErythPreCRMmm3_cusTrk.txt', |
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| 19 | 'cishg16' : 'ReglRegHBBhg16CusTrk.txt', |
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| 20 | 'cishg17' : 'ReglRegHBBhg17CusTrk.txt', |
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| 21 | 'exons' : 'ExonsKnownGenes_mm3.txt', |
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| 22 | 'krhg16' : 'known_regulatory_hg16.bed', |
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| 23 | 'krhg17' : 'known_regulatory_hg17.bed', |
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| 24 | 'tARhg16mmc' : 'hg16.mouse.t_AR.cold.bed', |
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| 25 | 'tARhg16mmm' : 'hg16.mouse.t_AR.medium.bed', |
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| 26 | 'tARhg16mmh' : 'hg16.mouse.t_AR.hot.bed', |
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| 27 | 'tARhg16rnc' : 'hg16.rat.t_AR.cold.bed', |
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| 28 | 'tARhg16rnm' : 'hg16.rat.t_AR.medium.bed', |
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| 29 | 'tARhg16rnh' : 'hg16.rat.t_AR.hot.bed', |
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| 30 | 'phastConsHg16' : 'phastConsMost_hg16.bed', |
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| 31 | 'omimhg16' : 'omimDisorders_hg16.tab', |
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| 32 | 'omimhg17' : 'omimDisorders_hg17.tab', |
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| 33 | |
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| 34 | } |
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| 35 | |
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| 36 | fname = id2name.get(dataid, '') |
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| 37 | if not fname: |
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| 38 | print 'Importing invalid data %s' % dataid |
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| 39 | sys.exit() |
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| 40 | else: |
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| 41 | print 'Imported %s' % fname |
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| 42 | |
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| 43 | # this path is hardcoded |
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| 44 | inp_name = os.path.join('database', 'import', fname) |
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| 45 | |
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| 46 | try: |
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| 47 | inp = open(inp_name, 'rt') |
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| 48 | except: |
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| 49 | print 'Could not find file %s' % inp_name |
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| 50 | sys.exit() |
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| 51 | |
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| 52 | out = open(out_name, 'wt') |
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| 53 | |
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| 54 | while 1: |
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| 55 | data = inp.read(BUFFER) |
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| 56 | if not data: |
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| 57 | break |
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| 58 | out.write(data) |
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| 59 | |
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| 60 | inp.close() |
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| 61 | out.close() |
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