def each_exon_rpkm(list_exons, bam_reader, library_size):
"""
Args:
list_exons = array of Exon objects
bam_reader = HTSeq.BAM_Reader instance, used to quantify the number of reads that map to SJ genomic range 'genomic_range' (command: bam_reader = HTSeq.BAM_Reader(path_to_bam_file) )
gene_sym = string that is the gene symbol -> used to determine which elements (introns) are constitutive for that gene.
library_size = integer that is the number of mapped reads in the sample
Function: returns the RPKM for all exons in array 'list_exons'
"""
#calculate expression of skipped exons
hash_exon_rpkm = {
} #k = string of position (format = chrom:start-end), v = hash that are 2 counts, RPKM from unique reads & all reads
for each_exon in list_exons:
exon_count_uniq = Isoform.quant_genes_rpkm(bam_reader,
each_exon.str_genomic_pos(),
True)
exon_count_all = Isoform.quant_genes_rpkm(bam_reader,
each_exon.str_genomic_pos(),
True)
str_exon_pos = each_exon.str_genomic_pos()
hash_exon_rpkm[str_exon_pos] = {}
hash_exon_rpkm[str_exon_pos]['rpkm_uniq'] = Isoform.calc_read_density(
exon_count_uniq, str_exon_pos, library_size)
hash_exon_rpkm[str_exon_pos]['rpkm_all'] = Isoform.calc_read_density(
exon_count_all, str_exon_pos, library_size)
return hash_exon_rpkm
def all_exons_rpkm(list_exons, bam_reader, library_size):
"""
Args:
list_exons = array of Exon objects
bam_reader = HTSeq.BAM_Reader instance, used to quantify the number of reads that map to SJ genomic range 'genomic_range' (command: bam_reader = HTSeq.BAM_Reader(path_to_bam_file) )
gene_sym = string that is the gene symbol -> used to determine which elements (introns) are constitutive for that gene.
library_size = integer that is the number of mapped reads in the sample
Function: returns the RPKM for all exons in array 'list_exons'
"""
#calculate expression of skipped exons
list_exons_rpkm = [] #records RPKM for all exons
for each_exon in list_exons:
exon_count = Isoform.quant_genes_rpkm(bam_reader,
each_exon.str_genomic_pos(),
True)
exon_rpkm = Isoform.calc_read_density(exon_count,
each_exon.str_genomic_pos(),
library_size)
list_exons_rpkm.append(exon_rpkm)
return list_exons_rpkm