#/usr/bin/python import sys from cruzdb import Genome sys.path.insert(0, "/home/mokha/Documents/Krauthammer_Lab/PythonClasses") from SVSv5 import Exon, Isoform, MultiIsoform, SpliceJunction, IsoformSJ print "------------ Algorithm: 160919_Isoform_1.py ------------" """ Reconstruct transcripts based on Splice Junctions """ #assign all splice junctions to specific gene: go through cruzdb & find end points for each gene --> assign # g = Genome( 'sqlite:////tmp/hg19.db' ) g = Genome('sqlite:////tmp/hg19_v2.db') Isoform.set_cruzdb(g) #retrieve gene & print information on it based on gene = g.refGene.filter_by(name2='BRAF').all() # all_genes = g.refGene.filter_by( name2 = 'TTN' ).first() # all_genes = g.refGene.filter_by( name2 = 'AGRN' ).all() # all_genes = g.refGene.filter_by( name2 = 'AGRN' ).first() # all_genes = g.refGene.filter_by( name2 = 'DIXDC1' ).all() for each_isoform in gene: obj_iso = Isoform(each_isoform.name) #print name print obj_iso.isoform_id, ":", obj_iso.gene_sym print "obj_iso = ", obj_iso
DIR_CURR = DIR_PROJ + "/PythonClasses/SVSv5" DIR_DATA = DIR_CURR + "/TestData" DIR_RESULTS = DIR_CURR + "/TestResults" # DIR_RESULTS = DIR_CURR + "/Results/160729_Analyze_KF" # DIR_RESULTS = DIR_CURR + "/Results/160731_Analyze_KF" # DIR_RESULTS = DIR_CURR + "/Results/160909_Analyze_KF" DIR_FUSION = DIR_PROJ + "/160510_GeneFusions" print "------------ TDD: 161002_IsoformFusion_1.py ------------" #set kinase gene annotation file KinaseFusion.set_kinasefile( DIR_FUSION + "/Data/160910_KinaseAnnots_hg38_Final.txt" ) obj_cruzdb = Genome( 'sqlite:////tmp/hg38_v2.db' ) #set cruzdb Genome database instance Isoform.set_cruzdb( obj_cruzdb ) #CASE: This returns "None" for the kinase domain for the kinase gene (TLK2 - NM_001284363) #Fusion - ASIC2:TLK2 hash_multi_isoform = { "orientation": 'fr', "chrom_start": 'chr17', "chrom_end": 'chr17', "pos_start": 34038904, "pos_end": 62565136, "read_span": 5, "read_matepair": 5, "read_matepair_break": 5 } obj_mif = MultiIsoformFusion( hash_multi_isoform ) #MIF = MultiIsoform Fusion instance for i, (k,v) in enumerate( obj_mif.isoform_fusions.iteritems() ): #k = isoformIDs in fusion (format: isoformID_1:isoformID_2), v = IsoformFusion instance