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https://github.com/galaxyproject/galaxy.git
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mvdbeek
53 lines
1.4 KiB
Python
53 lines
1.4 KiB
Python
#!/usr/bin/env python
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"""
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Connects to the URL specified and outputs builds available at that
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DSN in tabular format. UCSC Main gateway is used as default.
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build description
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"""
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import sys
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import xml.etree.ElementTree as ElementTree
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from galaxy.util import requests
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def getbuilds(url):
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try:
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text = requests.get(url).text
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except Exception:
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print("#Unable to open " + url)
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print("?\tunspecified (?)")
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sys.exit(1)
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try:
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tree = ElementTree.fromstring(text)
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except Exception:
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print("#Invalid xml passed back from " + url)
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print("?\tunspecified (?)")
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sys.exit(1)
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print("#Harvested from " + url)
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print("?\tunspecified (?)")
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for dsn in tree:
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build = dsn.find("SOURCE").attrib["id"]
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description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC", "").replace(" Genome at UCSC", "")
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fields = description.split(" ")
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temp = fields[0]
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for i in range(len(fields) - 1):
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if temp == fields[i + 1]:
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fields.pop(i + 1)
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else:
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temp = fields[i + 1]
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description = " ".join(fields)
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yield [build, description]
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if __name__ == "__main__":
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if len(sys.argv) > 1:
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URL = sys.argv[1]
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else:
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URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
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for build in getbuilds(URL):
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print(build[0] + "\t" + build[1] + " (" + build[0] + ")")
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