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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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