1 ###########################################################################
3 # C O P Y R I G H T N O T I C E #
4 # Copyright (c) 2003-13 by: #
5 # * California Institute of Technology #
7 # All Rights Reserved. #
9 # Permission is hereby granted, free of charge, to any person #
10 # obtaining a copy of this software and associated documentation files #
11 # (the "Software"), to deal in the Software without restriction, #
12 # including without limitation the rights to use, copy, modify, merge, #
13 # publish, distribute, sublicense, and/or sell copies of the Software, #
14 # and to permit persons to whom the Software is furnished to do so, #
15 # subject to the following conditions: #
17 # The above copyright notice and this permission notice shall be #
18 # included in all copies or substantial portions of the Software. #
20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
28 ###########################################################################
30 # data for Strongylocentrotus purpuratus
32 from cistematic.genomes import Genome
33 from os import environ
35 if environ.get("CISTEMATIC_ROOT"):
36 cisRoot = environ.get("CISTEMATIC_ROOT")
38 cisRoot = "/proj/genome"
40 geneDB = "%s/S_purpuratus/spurpuratus.genedb" % cisRoot
43 def buildSpurpuratusDB(db=geneDB):
44 chromoPath = "%s/download/Spur2.1_Nmasked.txt" % cisRoot
45 chromoOutPath = "/S_purpuratus/"
47 print "Creating database %s" % db
50 print "Loading genomic sequence"
51 loadChromosome(db, chromoPath, chromoOutPath)
53 print "Creating Indices"
56 print "Finished creating database %s" % db
59 spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
60 spGenome.createGeneDB(db)
63 def loadChromosome(db, chromPath, chromOutPath):
66 spGenome = Genome("spurpuratus", dbFile=db)
67 inFile = open(chromPath, "r")
68 header = inFile.readline()
72 fields = header.split()
73 if "purpuratus" in header:
76 idpart = fields[-1].strip()
78 parts = idpart.split("_")
80 currentLine = inFile.readline()
81 while currentLine != "" and currentLine[0] != ">":
82 lineSeq = currentLine.strip()
83 seqLen += len(lineSeq)
84 seqArray.append(lineSeq)
85 currentLine = inFile.readline()
87 seq = string.join(seqArray, "")
89 print "Added contig %s to database" % chromID
90 spGenome.addSequence(("spurpuratus", chromID), seq, "chromosome", str(seqLen))
91 spGenome.addChromosomeEntry(chromID, chromID, "db")
93 outFileName = "%s%s.bin" % (chromOutPath, chromID)
94 outFile = open("%s%s" % (cisRoot, outFileName), "w")
97 print "Added contig file %s to database" % outFileName
98 spGenome.addChromosomeEntry(chromID, outFileName, "file")
105 def createDBindices(db):
106 spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
107 spGenome.createIndices()