Mercurial > repos > yating-l > hubarchivecreator

annotate util/index/ExternIndex.py @ 82:62600ac1d0f7 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
author yating-l
date Wed, 27 Sep 2017 17:31:19 -0400
parents 4ca7cbf2d9b8
children 0bc486356e2a
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1 #!/usr/bin/python
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2 import collections
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3 import abc
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4 from abc import ABCMeta
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5
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6 class ExternIndex(object):
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7 __metaclass__ = ABCMeta
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8
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9 @abc.abstractmethod
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10 def __init__(self):
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11 """init"""
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12
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13 @abc.abstractmethod
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14 def setExtLink(self):
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15 """set external link"""
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17
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19
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20 '''
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21 @staticmethod
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22 def setExtLink(database, inputFile, extra_settings, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
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23 if "NCBI" in database:
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24 if not seqType:
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25 seqType = int(ExternIndex.getSeqType(inputFile))
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26 else:
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27 seqType = seqType
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28 if seqType < 0:
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29 print seqType
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30 raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
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31 if seqType == 2:
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32 extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
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33 elif seqType == 1:
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34 extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
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35 else:
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36 raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(seqType))
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37 elif "UniProt" in database:
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38 extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
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39 elif "FlyBase" in database:
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40 extra_settings["url"] = "http://flybase.org/reports/$$"
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41 else:
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42 extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
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43 extra_settings["urlLabel"] = database + " Details:"
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44 if useIframe:
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45 extra_settings["iframeUrl"] = extra_settings["url"]
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46 if not iframeHeight:
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47 iframeHeight = "600"
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48 if not iframeWidth:
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49 iframeWidth = "800"
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50 extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
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51
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52 @staticmethod
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53 def getSeqType(inputFile):
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54 with open(inputFile, "r") as bigpsl:
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55 sampleSeq = bigpsl.readline().split()
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56 if len(sampleSeq) == 25:
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57 return sampleSeq[-1]
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58 else:
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59 return "-1"
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60 '''