annotate util/index/DatabaseIndex.py @ 84:cb62314a6297 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Fri, 03 Nov 2017 17:08:19 -0400
parents 4ca7cbf2d9b8
children
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1 #!/usr/bin/python
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3 import collections
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4 from ExternIndex import ExternIndex
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6 class DatabaseIndex(ExternIndex):
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7 def __init__(self, database, **args):
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8 self.database = database
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9 self.seqType=args.get("seqType")
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10 self.useIframe=args.get("useIframe")
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11 self.iframeHeight=args.get("iframeHeight")
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12 self.iframeWidth=args.get("iframeWidth")
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14 def setExtLink(self):
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15 return self.setDatabaseLink(self.database, self.seqType, self.useIframe, self.iframeHeight, self.iframeWidth)
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17
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18 def setDatabaseLink(self, database, seqType=None, useIframe=None, iframeHeight=None, iframeWidth=None):
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19 database_settings = collections.OrderedDict()
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20 if "NCBI" in database:
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21 if not seqType:
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22 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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23 elif seqType == 2:
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24 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
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25 elif seqType == 1:
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26 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
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27 else:
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28 raise Exception("Sequence Type {0} is not valid, should be either protein (seqType==2) or nucleotide (seqType==1). Stopping the application".format(seqType))
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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29 elif "UniProt" in database:
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30 database_settings["url"] = "http://www.uniprot.org/uniprot/$$"
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31 elif "FlyBase" in database:
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32 database_settings["url"] = "http://flybase.org/reports/$$"
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33 else:
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34 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
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35 database_settings["urlLabel"] = database + " Details:"
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36 if useIframe or useIframe is None:
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37 database_settings["iframeUrl"] = database_settings["url"]
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38 if not iframeHeight:
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39 iframeHeight = "600"
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40 if not iframeWidth:
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41 iframeWidth = "800"
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42 database_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
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43 return database_settings
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44