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]) ########################