diff util/index/ExternIndex.py @ 3:fa990284327b draft default tip

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty

--- a/util/index/ExternIndex.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/util/index/ExternIndex.py	Mon Oct 30 11:58:31 2017 -0400
@@ -13,48 +13,4 @@
     @abc.abstractmethod
     def setExtLink(self):
         """set external link"""
-        
-    
-    
-
-    '''
-    @staticmethod 
-    def setExtLink(database, inputFile, extra_settings, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
-        if "NCBI" in database:
-            if not seqType:
-                seqType = int(ExternIndex.getSeqType(inputFile))
-            else:
-                seqType = seqType
-            if seqType < 0:
-                print seqType
-                raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
-            if seqType == 2:
-                extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
-            elif seqType == 1:
-                extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
-            else:
-                raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(seqType))
-        elif "UniProt" in database:
-            extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
-        elif "FlyBase" in database:
-            extra_settings["url"] = "http://flybase.org/reports/$$"
-        else:
-            extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
-        extra_settings["urlLabel"] = database + " Details:"
-        if useIframe:
-            extra_settings["iframeUrl"] = extra_settings["url"]
-            if not iframeHeight:
-                iframeHeight = "600"
-            if not iframeWidth:
-                iframeWidth = "800"
-            extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
-
-    @staticmethod
-    def getSeqType(inputFile):
-        with open(inputFile, "r") as bigpsl:
-            sampleSeq = bigpsl.readline().split()
-        if len(sampleSeq) == 25:
-            return sampleSeq[-1]
-        else:
-            return "-1"        
-    '''
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+        
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