- cfGenome.createIndices()
-
-
-def buildDogDB(db=geneDB):
- genePath = "%s/download/seq_gene.md" % cisRoot
- chromos = {"1": "%s/download/chr1.fa" % cisRoot,
- "2": "%s/download/chr2.fa" % cisRoot,
- "3": "%s/download/chr3.fa" % cisRoot,
- "4": "%s/download/chr4.fa" % cisRoot,
- "5": "%s/download/chr5.fa" % cisRoot,
- "6": "%s/download/chr6.fa" % cisRoot,
- "7": "%s/download/chr7.fa" % cisRoot,
- "8": "%s/download/chr8.fa" % cisRoot,
- "9": "%s/download/chr9.fa" % cisRoot,
- "10": "%s/download/chr10.fa" % cisRoot,
- "11": "%s/download/chr11.fa" % cisRoot,
- "12": "%s/download/chr12.fa" % cisRoot,
- "13": "%s/download/chr13.fa" % cisRoot,
- "14": "%s/download/chr14.fa" % cisRoot,
- "15": "%s/download/chr15.fa" % cisRoot,
- "16": "%s/download/chr16.fa" % cisRoot,
- "17": "%s/download/chr17.fa" % cisRoot,
- "18": "%s/download/chr18.fa" % cisRoot,
- "19": "%s/download/chr19.fa" % cisRoot,
- "20": "%s/download/chr20.fa" % cisRoot,
- "21": "%s/download/chr21.fa" % cisRoot,
- "22": "%s/download/chr22.fa" % cisRoot,
- '23': "%s/download/chr23.fa" % cisRoot,
- "24": "%s/download/chr24.fa" % cisRoot,
- "25": "%s/download/chr25.fa" % cisRoot,
- "26": "%s/download/chr26.fa" % cisRoot,
- "27": "%s/download/chr27.fa" % cisRoot,
- "28": "%s/download/chr28.fa" % cisRoot,
- "29": "%s/download/chr29.fa" % cisRoot,
- "30": "%s/download/chr30.fa" % cisRoot,
- "31": "%s/download/chr31.fa" % cisRoot,
- "32": "%s/download/chr32.fa" % cisRoot,
- "33": "%s/download/chr33.fa" % cisRoot,
- "34": "%s/download/chr34.fa" % cisRoot,
- "35": "%s/download/chr35.fa" % cisRoot,
- "36": "%s/download/chr36.fa" % cisRoot,
- "37": "%s/download/chr37.fa" % cisRoot,
- "38": "%s/download/chr38.fa" % cisRoot,
- "X": "%s/download/chrX.fa" % cisRoot,
- "Un": "%s/download/chrUn.fa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)