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1 #!/usr/bin/env python
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2 import urllib
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3 import sys, os
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4
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5 assert sys.version_info[:2] >= ( 2, 4 )
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6
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7 CHUNK = 2**20 # 1Mb
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8 MAXSIZE = CHUNK * 100
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9 if __name__ == '__main__':
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10
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11 if len(sys.argv) != 3:
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12 print 'Usage ucsc.py input_params output_file'
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13 sys.exit()
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14
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15 inp_file = sys.argv[1]
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16 out_file = sys.argv[2]
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17
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18 DEFAULT_URL = "http://genome.ucsc.edu/hgTables?"
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19
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20 # this must stay a list to allow multiple selections for the same widget name (checkboxes)
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21 params = []
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22 for line in file(inp_file):
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23 line = line.strip()
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24 if line:
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25 parts = line.split('=')
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26 if len(parts) == 0:
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27 key = ""
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28 value = ""
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29 elif len(parts) == 1:
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30 key = parts[0]
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31 value = ""
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32 else:
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33 key = parts[0]
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34 value = parts[1]
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35 if key == 'display':
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36 print value
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37 # get url from params, refered from proxy.py, initialized by the tool xml
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38 elif key == 'proxy_url':
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39 DEFAULT_URL = value
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40 else:
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41 params.append( (key, value) )
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42
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43 #print params
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44
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45 encoded_params = urllib.urlencode(params)
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46 url = DEFAULT_URL + encoded_params
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47
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48 #print url
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49
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50 page = urllib.urlopen(url)
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51
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52 fp = open(out_file, 'wt')
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53 size = 0
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54 while 1:
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55 data = page.read(CHUNK)
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56 if not data:
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57 break
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58 if size > MAXSIZE:
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59 fp.write('----- maximum datasize exceeded ---\n')
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60 break
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61 size += len(data)
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62 fp.write(data)
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63
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64 fp.close()
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65
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