Mercurial > repos > yating-l > jbrowsearchivecreator

comparison util/index/DatabaseIndex.py @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
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children 3f9971a91096
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5:e762f4b9e4bd 6:237707a6b74d
1 #!/usr/bin/python
2
3 import collections
4 from ExternIndex import ExternIndex
5
6 class DatabaseIndex(ExternIndex):
7 def __init__(self, database, **args):
8 self.database = database
9 self.seqType=args.get("seqType")
10 self.useIframe=args.get("useIframe")
11 self.iframeHeight=args.get("iframeHeight")
12 self.iframeWidth=args.get("iframeWidth")
13
14 def setExtLink(self):
15 return self.setDatabaseLink(self.database, self.seqType, self.useIframe, self.iframeHeight, self.iframeWidth)
16
17
18 def setDatabaseLink(self, database, seqType=None, useIframe=None, iframeHeight=None, iframeWidth=None):
19 database_settings = collections.OrderedDict()
20 if "NCBI" in database:
21 if not seqType:
22 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
23 elif seqType == 2:
24 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
25 elif seqType == 1:
26 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
27 else:
28 raise Exception("Sequence Type {0} is not valid, should be either protein (seqType==2) or nucleotide (seqType==1). Stopping the application".format(seqType))
29 elif "UniProt" in database:
30 database_settings["url"] = "http://www.uniprot.org/uniprot/$$"
31 elif "FlyBase" in database:
32 database_settings["url"] = "http://flybase.org/reports/$$"
33 else:
34 database_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
35 database_settings["urlLabel"] = database + " Details:"
36 if useIframe or useIframe is None:
37 database_settings["iframeUrl"] = database_settings["url"]
38 if not iframeHeight:
39 iframeHeight = "600"
40 if not iframeWidth:
41 iframeWidth = "800"
42 database_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
43 return database_settings
44