a = open(File, 'r')
for l in a.read().split('\n'):
if l.strip() == "": continue
lsep = l.split('\t')
if lsep[3] in ['+', '-']:
bed1 = Bed(lsep[0:3], strand=lsep[3])
bed2 = Bed(lsep[s:(s + 3)], strand=lsep[s + 3])
else:
bed1 = Bed(lsep[0:3])
bed2 = Bed(lsep[s:(s + 3)])
yield (bed1, bed2, lsep)
# annotation files
db = "/home/yu68/bharat-interaction/new_lincRNA_data/all_RNAs-rRNA_repeat.txt"
db_detail = "/home/yu68/bharat-interaction/new_lincRNA_data/Ensembl_mm9.genebed"
db_repeat = "/home/yu68/bharat-interaction/new_lincRNA_data/mouse.repeat.txt"
print >> sys.stderr, "Indexing annotation files..."
ref_allRNA = DBI.init(
db, "bed") # the DBI init file for bed6 file of all kinds of RNA
ref_detail = DBI.init(
db_detail, "bed"
) # the DBI init file for bed12 file of lincRNA and mRNA with intron, exon, UTR
ref_repeat = DBI.init(db_repeat, "bed")
print >> sys.stderr, "Start to update..."
for l in read_interaction(sys.argv[1], 9):
l[2][5:8] = annotation(l[0], ref_allRNA, ref_detail, ref_repeat)
l[2][14:17] = annotation(l[1], ref_allRNA, ref_detail, ref_repeat)
print "\t".join(l[2])
s: start column number for second part of interaction
'''
a=open(File,'r')
for l in a.read().split('\n'):
if l.strip()=="": continue
lsep=l.split('\t')
if lsep[3] in ['+','-']:
bed1=Bed(lsep[0:3],strand=lsep[3])
bed2=Bed(lsep[s:(s+3)],strand=lsep[s+3])
else:
bed1=Bed(lsep[0:3])
bed2=Bed(lsep[s:(s+3)])
yield (bed1,bed2,lsep)
# annotation files
db="/home/yu68/bharat-interaction/new_lincRNA_data/all_RNAs-rRNA_repeat.txt"
db_detail="/home/yu68/bharat-interaction/new_lincRNA_data/Ensembl_mm9.genebed"
db_repeat="/home/yu68/bharat-interaction/new_lincRNA_data/mouse.repeat.txt"
print >>sys.stderr, "Indexing annotation files..."
ref_allRNA=DBI.init(db,"bed") # the DBI init file for bed6 file of all kinds of RNA
ref_detail=DBI.init(db_detail,"bed") # the DBI init file for bed12 file of lincRNA and mRNA with intron, exon, UTR
ref_repeat=DBI.init(db_repeat,"bed")
print >>sys.stderr, "Start to update..."
for l in read_interaction(sys.argv[1],7):
l[2][3:6] = annotation(l[0],ref_allRNA,ref_detail,ref_repeat)
l[2][10:13] = annotation(l[1],ref_allRNA,ref_detail,ref_repeat)
print "\t".join(l[2])
s: start column number for second part of interaction
'''
a=open(File,'r')
for l in a.read().split('\n'):
if l.strip()=="": continue
lsep=l.split('\t')
if lsep[3] in ['+','-']:
bed1=Bed(lsep[0:3],strand=lsep[3])
bed2=Bed(lsep[s:(s+3)],strand=lsep[s+3])
else:
bed1=Bed(lsep[0:3])
bed2=Bed(lsep[s:(s+3)])
yield (bed1,bed2,lsep)
# annotation files
db="/home/yu68/bharat-interaction/new_lincRNA_data/all_RNAs-rRNA_repeat.txt"
db_detail="/home/yu68/bharat-interaction/new_lincRNA_data/Ensembl_mm9.genebed"
db_repeat="/home/yu68/bharat-interaction/new_lincRNA_data/mouse.repeat.txt"
print >>sys.stderr, "Indexing annotation files..."
ref_allRNA=DBI.init(db,"bed") # the DBI init file for bed6 file of all kinds of RNA
ref_detail=DBI.init(db_detail,"bed") # the DBI init file for bed12 file of lincRNA and mRNA with intron, exon, UTR
ref_repeat=DBI.init(db_repeat,"bed")
print >>sys.stderr, "Start to update..."
for l in read_interaction(sys.argv[1],9):
l[2][5:8] = annotation(l[0],ref_allRNA,ref_detail,ref_repeat)
l[2][14:17] = annotation(l[1],ref_allRNA,ref_detail,ref_repeat)
print "\t".join(l[2])
