/tools/data_source/import.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 61 lines · 42 code · 13 blank · 6 comment · 5 complexity · 5dfa55d2630b7ca909ce0decdffc86e7 MD5 · raw file
- #!/usr/bin/env python
- """
- Script that imports locally stored data as a new dataset for the user
- Usage: import id outputfile
- """
- import sys, os
- assert sys.version_info[:2] >= ( 2, 4 )
- BUFFER = 1048576
- dataid = sys.argv[1]
- out_name = sys.argv[2]
- id2name = {
- 'eryth' : 'ErythPreCRMmm3_cusTrk.txt',
- 'cishg16' : 'ReglRegHBBhg16CusTrk.txt',
- 'cishg17' : 'ReglRegHBBhg17CusTrk.txt',
- 'exons' : 'ExonsKnownGenes_mm3.txt',
- 'krhg16' : 'known_regulatory_hg16.bed',
- 'krhg17' : 'known_regulatory_hg17.bed',
- 'tARhg16mmc' : 'hg16.mouse.t_AR.cold.bed',
- 'tARhg16mmm' : 'hg16.mouse.t_AR.medium.bed',
- 'tARhg16mmh' : 'hg16.mouse.t_AR.hot.bed',
- 'tARhg16rnc' : 'hg16.rat.t_AR.cold.bed',
- 'tARhg16rnm' : 'hg16.rat.t_AR.medium.bed',
- 'tARhg16rnh' : 'hg16.rat.t_AR.hot.bed',
- 'phastConsHg16' : 'phastConsMost_hg16.bed',
- 'omimhg16' : 'omimDisorders_hg16.tab',
- 'omimhg17' : 'omimDisorders_hg17.tab',
- }
- fname = id2name.get(dataid, '')
- if not fname:
- print 'Importing invalid data %s' % dataid
- sys.exit()
- else:
- print 'Imported %s' % fname
- # this path is hardcoded
- inp_name = os.path.join('database', 'import', fname)
- try:
- inp = open(inp_name, 'rt')
- except:
- print 'Could not find file %s' % inp_name
- sys.exit()
- out = open(out_name, 'wt')
- while 1:
- data = inp.read(BUFFER)
- if not data:
- break
- out.write(data)
- inp.close()
- out.close()