BASE="/home/bmajoros/1000G/assembly/combined"
FILES=glob.glob(BASE+"/*/*.ice9")
for file in FILES:
print(file)
parser=EssexParser(file)
while(True):
root=parser.nextElem()
if(not root): break
alts=root.pathQuery("report/status/alternate-structures")
if(not alts): continue
transcripts=alts.findChildren("transcript")
scores={}
numCryptic=0
for transcript in transcripts:
change=transcript.getAttribute("structure-change")
score=transcript.getAttribute("score")
if(change not in scores): scores[change]=0.0
scores[change]+=float(score)
numCryptic+=1
if(len(scores)!=2): continue
skippingScore=scores["exon-skipping"]
crypticScore=scores["cryptic-site"]
print(root.getAttribute("substrate"),
root.getAttribute("transcript-ID"),
skippingScore,crypticScore,numCryptic,flush=True)
parser.close()
