def indexVariants(variants):
'''build index of variants for ranged retrieval.'''
index = ncl.NCL()
for start, end, reference, action, has_wildtype, variantseqs in variants:
index.add(start, end, (reference, action, has_wildtype, variantseqs))
return index
def buildIndex(self, filename):
"""read and index."""
idx = {}
infile = IOTools.openFile(filename, "r")
for e in GTF.readFromFile(infile):
if e.contig not in idx: idx[e.contig] = NCL.NCLSimple()
idx[e.contig].add(e.start, e.end)
infile.close()
return idx
def nclpy_create_on_disk_and_flush(segmenter):
index = ncl.NCL(filestem="tmp", force=True)
for id, coords in enumerate(segmenter):
index.add(coords[0], coords[1], id)
del index
return ncl.NCL(filestem="tmp")
def nclpy_create(segmenter):
index = ncl.NCL()
for id, coords in enumerate(segmenter):
index.add(coords[0], coords[1], id)
return index
def ncl_create(segmenter):
index = ncl.IntervalDB()
index.fromlist([(coords[0], coords[1], id)
for id, coords in enumerate(segmenter)])
return index