#/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