[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Connects to the URL specified and outputs builds available at that |
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| 5 | DSN in tabular format. USCS Test gateway is used as default. |
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| 6 | build description |
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| 7 | """ |
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| 8 | |
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| 9 | import sys |
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| 10 | import urllib |
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| 11 | if sys.version_info[:2] >= ( 2, 5 ): |
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| 12 | import xml.etree.ElementTree as ElementTree |
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| 13 | else: |
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| 14 | from galaxy import eggs |
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| 15 | import pkg_resources; pkg_resources.require( "elementtree" ) |
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| 16 | from elementtree import ElementTree |
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| 17 | |
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| 18 | URL = "http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" |
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| 19 | |
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| 20 | def getbuilds(url): |
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| 21 | try: |
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| 22 | page = urllib.urlopen(URL) |
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| 23 | except: |
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| 24 | print "#Unable to open " + URL |
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| 25 | print "?\tunspecified (?)" |
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| 26 | sys.exit(1) |
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| 27 | |
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| 28 | text = page.read() |
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| 29 | try: |
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| 30 | tree = ElementTree.fromstring(text) |
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| 31 | except: |
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| 32 | print "#Invalid xml passed back from " + URL |
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| 33 | print "?\tunspecified (?)" |
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| 34 | sys.exit(1) |
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| 35 | |
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| 36 | print "#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" |
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| 37 | print "?\tunspecified (?)" |
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| 38 | for dsn in tree: |
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| 39 | build = dsn.find("SOURCE").attrib['id'] |
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| 40 | description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC","").replace(" Genome at UCSC","") |
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| 41 | |
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| 42 | fields = description.split(" ") |
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| 43 | temp = fields[0] |
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| 44 | for i in range(len(fields)-1): |
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| 45 | if temp == fields[i+1]: |
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| 46 | fields.pop(i+1) |
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| 47 | else: |
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| 48 | temp = fields[i+1] |
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| 49 | description = " ".join(fields) |
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| 50 | yield [build,description] |
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| 51 | |
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| 52 | if __name__ == "__main__": |
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| 53 | if len(sys.argv) > 1: |
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| 54 | URL = sys.argv[1] |
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| 55 | for build in getbuilds(URL): |
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| 56 | print build[0]+"\t"+build[1]+" ("+build[0]+")" |
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| 57 | |
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