with_statement)
from builtins import (bytes, dict, int, list, object, range, str, ascii, chr,
hex, input, next, oct, open, pow, round, super, filter,
map, zip)
# The above imports should allow this program to run in both Python 2 and
# Python 3. You might need to update your version of module "future".
from GffTranscriptReader import GffTranscriptReader
#filename="/home/bmajoros/1000G/assembly/local-genes.gff"
#filename="/home/bmajoros/1000G/assembly/tmp.gff"
#filename="test/data/tmp.gff"
#filename="test/data/local-genes.gff"
filename = "/home/bmajoros/ensembl/protein-coding.gff"
reader = GffTranscriptReader()
genes = reader.loadGenes(filename)
for gene in genes:
exons = gene.getMergedExons()
unmerged = 0
for transcript in gene.transcripts:
unmerged += len(transcript.getRawExons())
print(unmerged, "exons merged to", len(exons))
#for i in range(len(exons)):
# print("MERGED TO:",exons[i].begin,exons[i].end)
# print()
#transcripts=reader.loadGFF(filename)
#for transcript in transcripts:
#print(transcript.getID())
#gff=transcript.toGff()
#print(gff)
