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)