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