-
-
-def buildChickenDB(db=geneDB):
- genePath = "%s/download/seq_gene.md" % cisRoot
- goDefPath = "%s/download/GO.terms_and_ids" % cisRoot # ftp://ftp.geneontology.org/pub/go/doc/GO.terms_and_ids
- goPath = "%s/download/gene2go" % cisRoot # ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz
- 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,
- "32": "%s/download/chr32.fa" % cisRoot,
- "W": "%s/download/chrW.fa" % cisRoot,
- "Z": "%s/download/chrZ.fa" % cisRoot,
- "M": "%s/download/chrM.fa" % cisRoot,
- "E22C19W28_E50C23": "%s/download/chrE22C19W28_E50C23.fa" % cisRoot,
- "E64": "%s/download/chrE64.fa" % cisRoot,
- "1_random": "%s/download/chr1_random.fa" % cisRoot,
- "2_random": "%s/download/chr2_random.fa" % cisRoot,
- "4_random": "%s/download/chr4_random.fa" % cisRoot,
- "5_random": "%s/download/chr5_random.fa" % cisRoot,
- "6_random": "%s/download/chr6_random.fa" % cisRoot,
- "7_random": "%s/download/chr7_random.fa" % cisRoot,
- "8_random": "%s/download/chr8_random.fa" % cisRoot,
- "10_random": "%s/download/chr10_random.fa" % cisRoot,
- "11_random": "%s/download/chr11_random.fa" % cisRoot,
- "12_random": "%s/download/chr12_random.fa" % cisRoot,
- "13_random": "%s/download/chr13_random.fa" % cisRoot,
- "16_random": "%s/download/chr16_random.fa" % cisRoot,
- "17_random": "%s/download/chr17_random.fa" % cisRoot,
- "18_random": "%s/download/chr18_random.fa" % cisRoot,
- "20_random": "%s/download/chr20_random.fa" % cisRoot,
- "22_random": "%s/download/chr22_random.fa" % cisRoot,
- "25_random": "%s/download/chr25_random.fa" % cisRoot,
- "28_random": "%s/download/chr28_random.fa" % cisRoot,
- "Un_random": "%s/download/chrUn_random.fa" % cisRoot,
- "W_random": "%s/download/chrW_random.fa" % cisRoot,
- "E64_random": "%s/download/chrE64_random.fa" % cisRoot,
- "Z_random": "%s/download/chrZ_random.fa" % cisRoot,
- "E22C19W28_E50C23_random": "%s/download/chrE22C19W28_E50C23_random.fa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
-
- #print "Adding gene annotations"
- #loadGeneAnnotations(db, annotPath)
-
- print "Adding gene features"
- loadGeneFeatures(db, genePath)
-
- for chromID in chromos.keys():
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/G_gallus/chromo%s.bin" % chromID)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file