erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / genomes / spurpuratus.py

diff --git a/cistematic/genomes/spurpuratus.py b/cistematic/genomes/spurpuratus.py
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+###########################################################################
+#                                                                         #
+# C O P Y R I G H T   N O T I C E                                         #
+#  Copyright (c) 2003-10 by:                                              #
+#    * California Institute of Technology                                 #
+#                                                                         #
+#    All Rights Reserved.                                                 #
+#                                                                         #
+# Permission is hereby granted, free of charge, to any person             #
+# obtaining a copy of this software and associated documentation files    #
+# (the "Software"), to deal in the Software without restriction,          #
+# including without limitation the rights to use, copy, modify, merge,    #
+# publish, distribute, sublicense, and/or sell copies of the Software,    #
+# and to permit persons to whom the Software is furnished to do so,       #
+# subject to the following conditions:                                    #
+#                                                                         #
+# The above copyright notice and this permission notice shall be          #
+# included in all copies or substantial portions of the Software.         #
+#                                                                         #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
+# SOFTWARE.                                                               #
+###########################################################################
+#
+# data for Strongylocentrotus purpuratus
+import string
+from cistematic.genomes import Genome
+from os import environ
+
+if environ.get("CISTEMATIC_ROOT"):
+    cisRoot = environ.get("CISTEMATIC_ROOT") 
+else:
+    cisRoot = "/proj/genome"
+
+geneDB = "%s/S_purpuratus/spurpuratus.genedb" % cisRoot
+
+
+def loadChromosome(db, chromPath, chromOutPath):
+    seqArray = []
+    seqLen = 0
+    spGenome = Genome("spurpuratus", dbFile=db)
+    inFile = open(chromPath, "r")
+    header = inFile.readline()
+    while header != "":
+        seqArray = []
+        seqLen = 0
+        fields = header.split()
+        if "purpuratus" in header:
+            idpart = fields[3]
+        else:
+            idpart = fields[-1].strip()
+
+        parts = idpart.split("_")
+        chromID = parts[-1]
+        currentLine = inFile.readline()
+        while currentLine != "" and currentLine[0] != ">":
+            lineSeq = currentLine.strip()
+            seqLen += len(lineSeq)
+            seqArray.append(lineSeq)
+            currentLine = inFile.readline()
+
+        seq = string.join(seqArray, "")
+        if seqLen < 50000:
+            print "Added contig %s to database" % chromID
+            spGenome.addSequence(("spurpuratus", chromID), seq, "chromosome", str(seqLen))
+            spGenome.addChromosomeEntry(chromID, chromID, "db")
+        else:
+            outFileName = "%s%s.bin" % (chromOutPath, chromID)
+            outFile = open("%s%s" % (cisRoot, outFileName), "w")
+            outFile.write(seq)
+            outFile.close()
+            print "Added contig file %s to database" % outFileName
+            spGenome.addChromosomeEntry(chromID, outFileName, "file")
+
+        header = currentLine
+
+    inFile.close()
+
+
+def createDBFile(db):
+    spGenome = Genome("spurpuratus", version="2.1",  dbFile=db)
+    spGenome.createGeneDB(db)
+
+
+def createDBindices(db):
+    spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
+    spGenome.createIndices()
+
+
+def buildSpurpuratusDB(db=geneDB):
+    chromoPath = "%s/download/Spur2.1_Nmasked.txt" % cisRoot
+    chromoOutPath = "/S_purpuratus/"
+
+    print "Creating database %s" % db
+    createDBFile(db)
+
+    print "Loading genomic sequence" 
+    loadChromosome(db, chromoPath, chromoOutPath)
+
+    print "Creating Indices"
+    createDBindices(db)
+
+    print "Finished creating database %s" % db
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