Dear all,
I am interested in the splicing pattern query by using pygr. I have
been suggested by Dr. Namshin Kim to post a question here.
How to build a spliceGraph database from a new gene dataset, like the
knownGene, knownCanonical, knownIsoforms in hg18 from UCSC database?
I also have a few questions about the code from pygr/tests/old/
splicegraph_jan06.py as below.
---
def buildClusterSpliceGraph(c,alt5,alt3):
"""use exon/splice start and end positions to build splice graph
for a cluster c.
Also finds exons that share same start (but differ at end:
alt5), or
share the same end (but differ at start: alt3).
"""
for e in c.exons:
---
clusterExons=dictGraph()
clusterSplices=dictGraph()
spliceGraph=dictGraph()
alt5=dictGraph()
alt3=dictGraph()
---
And what is the content of clusterExons? Does it mean all the exons in
a cluster of genes which have overlapping between them? How to build
the clusterExons, clusterSplices from gene annotation files, not from
database?
What is the class of 'c'? Is it necessary to build spliceGraph by
cluster?
Thank you very much in advance!
Best regards,
Yu Zhou
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