def py2c_gene(py_gene):
"""
Convert a Python Gene object to a C gene object for use
with C MISO.
"""
# Description of exon lens
CMISO_exon_lens = tuple([(part.start, part.end) for part in py_gene.parts])
# Description of isoforms of gene
isoforms_desc = []
for isoform in py_gene.isoforms:
curr_iso_desc = tuple([py_gene.parts.index(iso_part) for iso_part in isoform.parts])
isoforms_desc.append(curr_iso_desc)
CMISO_isoforms_desc = tuple(isoforms_desc)
c_gene = pysplicing.createGene(CMISO_exon_lens, CMISO_isoforms_desc)
return c_gene
def py2c_gene(py_gene):
"""
Convert a Python Gene object to a C gene object for use
with C MISO.
"""
# Description of exon lens
CMISO_exon_lens = tuple([(part.start, part.end) \
for part in py_gene.parts])
# Description of isoforms of gene
isoforms_desc = []
for isoform in py_gene.isoforms:
curr_iso_desc = tuple([py_gene.parts.index(iso_part) \
for iso_part in isoform.parts])
isoforms_desc.append(curr_iso_desc)
CMISO_isoforms_desc = tuple(isoforms_desc)
c_gene = pysplicing.createGene(CMISO_exon_lens, CMISO_isoforms_desc)
return c_gene
##
## Test Pysplicing (fastmiso)
##
import misopy
import misopy.gff_utils
import pysplicing
gene = pysplicing.createGene(((1, 100), (201, 300), (401, 500)),
((0, 1), (0, 2), (0, 1, 2)))
pysplicing.noIso(gene)
pysplicing.isoLength(gene)
reads = pysplicing.simulateReads(gene, 0L, (0.2, 0.3, 0.5), 2000L, 33L)
print "Reads: ", reads[1]
print "Cigars: ", reads[2]
# Load BAM file
print reads[1], type(reads[1])
results = pysplicing.MISO(gene, 0L, reads[1], reads[2], 33L, 5000L, 500L, 10L,
(1.0, 1.0, 1.0))
print "Results:", results[0]
# est2 = pysplicing.solveIsoGene(gene, 0L, 33L, reads[1], reads[2])
########################
##
## Test Pysplicing (fastmiso)
##
import misopy
import misopy.gff_utils
import pysplicing
gene = pysplicing.createGene( ((1,100), (201,300), (401,500)),
((0,1), (0,2), (0,1,2)) )
pysplicing.noIso(gene)
pysplicing.isoLength(gene)
reads = pysplicing.simulateReads(gene, 0L, (0.2,0.3,0.5), 2000L, 33L)
print "Reads: ", reads[1]
print "Cigars: ",reads[2]
# Load BAM file
print reads[1], type(reads[1])
results = pysplicing.MISO(gene, 0L, reads[1], reads[2], 33L, 5000L, 500L, 10L,
(1.0, 1.0, 1.0))
print "Results:" , results[0]
# est2 = pysplicing.solveIsoGene(gene, 0L, 33L, reads[1], reads[2])
########################