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63 lines
1.5 KiB
Python
63 lines
1.5 KiB
Python
#!/usr/bin/env python
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"""
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Script that imports locally stored data as a new dataset for the user
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Usage: import id outputfile
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"""
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from __future__ import print_function
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import os
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import sys
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assert sys.version_info[:2] >= (2, 6)
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BUFFER = 1048576
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dataid = sys.argv[1]
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out_name = sys.argv[2]
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id2name = {
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'eryth' : 'ErythPreCRMmm3_cusTrk.txt',
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'cishg16' : 'ReglRegHBBhg16CusTrk.txt',
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'cishg17' : 'ReglRegHBBhg17CusTrk.txt',
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'exons' : 'ExonsKnownGenes_mm3.txt',
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'krhg16' : 'known_regulatory_hg16.bed',
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'krhg17' : 'known_regulatory_hg17.bed',
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'tARhg16mmc' : 'hg16.mouse.t_AR.cold.bed',
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'tARhg16mmm' : 'hg16.mouse.t_AR.medium.bed',
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'tARhg16mmh' : 'hg16.mouse.t_AR.hot.bed',
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'tARhg16rnc' : 'hg16.rat.t_AR.cold.bed',
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'tARhg16rnm' : 'hg16.rat.t_AR.medium.bed',
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'tARhg16rnh' : 'hg16.rat.t_AR.hot.bed',
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'phastConsHg16' : 'phastConsMost_hg16.bed',
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'omimhg16' : 'omimDisorders_hg16.tab',
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'omimhg17' : 'omimDisorders_hg17.tab',
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}
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fname = id2name.get(dataid, '')
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if not fname:
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print('Importing invalid data %s' % dataid)
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sys.exit()
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else:
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print('Imported %s' % fname)
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# this path is hardcoded
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inp_name = os.path.join('database', 'import', fname)
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try:
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inp = open(inp_name, 'rt')
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except Exception:
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print('Could not find file %s' % inp_name)
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sys.exit()
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out = open(out_name, 'wt')
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while 1:
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data = inp.read(BUFFER)
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if not data:
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break
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out.write(data)
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inp.close()
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out.close()
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