assert gt_tuple_pos == [p for p,e in enumerate(currentDon) if e != -inf and p > 0], pdb.set_trace()
assert len(currentAcc) == len(currentDon)
+ pdb.set_trace()
+
return genomicSeq, currentAcc, currentDon
# build reverse complement if on negative strand
fn = 'chr%d.dna.flat' % chr
filename = os.path.join(dna_flat_files,fn)
cmd = 'wc -c %s | cut -f1 -d \' \'' % filename
- #print cmd
import subprocess
obj = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
out,err = obj.communicate()
print 'Error occurred while trying to obtain file size'
end = int(out)
- #print 'size is %d' % end
-
- intervalBegin = genomicSeq_start-100
- intervalEnd = genomicSeq_stop+100
-
- #print 'before getSpliceScores'
- #print intervalBegin ,intervalEnd
+ intervalBegin = genomicSeq_start#-100
+ intervalEnd = genomicSeq_stop#+100
total_size = end
currentAcc, currentDon = getSpliceScores(chr,strand,intervalBegin,intervalEnd,total_size)
- currentAcc = currentAcc[100:-98]
+ #currentAcc = currentAcc[100:-98]
currentAcc = currentAcc[1:]
- currentDon = currentDon[100:-100]
+ #currentDon = currentDon[100:-100]
length = len(genomicSeq)
currentAcc = currentAcc[:length]
+ currentAcc = currentAcc+[-inf]*(length-len(currentAcc))
currentDon = currentDon+[-inf]*(length-len(currentDon))
assert ag_tuple_pos == [p for p,e in enumerate(currentAcc) if e != -inf and p > 1], pdb.set_trace()
assert gt_tuple_pos == [p for p,e in enumerate(currentDon) if e != -inf and p > 0], pdb.set_trace()
- assert len(currentAcc) == len(currentDon)
+ assert len(currentAcc) == len(currentDon), pdb.set_trace()
return genomicSeq, currentAcc, currentDon