-def loadChromosomes(db, inPath, chromOutPath):
- crGenome = Genome("cremanei", dbFile=db)
- scontigList = os.listdir(inPath)
- for scontig in scontigList:
- seq = ''
- seqArray = []
- seqLen = 0
- inFile = open("%s/%s" % (inPath, scontig), "r")
- index = 0
- header = inFile.readline()
- chromID = header.strip()[1:]
- while header != "":
- seqArray = []
- seqLen = 0
- currentLine = inFile.readline()
- while currentLine != "" and currentLine[0] != ">":
- lineSeq = currentLine.strip()
- seqLen += len(lineSeq)
- seqArray.append(lineSeq)
- currentLine = inFile.readline()
+def buildCremaneiDB(db=geneDB):
+ gffPath = "%s/download/cr01_wu_merged_gff" % cisRoot # using 20050824 version
+ chromoPath = "%s/download/sctg_masked_seqs/seqs" % cisRoot
+ chromoOutPath = "/C_remanei/"