view seg2matrix/CGData/RefGene.py @ 37:e81019e3ac99

Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format

import csv
import re
import CGData

#column definitions for the current refGene_hg18.table
COL_CHROM = 2
COL_STRAND = 3
COL_START = 4
COL_END = 5
COL_CDSSTART = 6
COL_CDSEND = 7
COL_EXCOUNT = 8
COL_EXSTART = 9
COL_EXEND = 10
COL_HUGO = 12


#sometimes the ref table ends with a comma, which makes
#arrays that end with '' when you split
re_comma_end = re.compile(r',$')


class GeneInfo(object):
    """
    Class to hold information about gene, including exon start/stops
    """

    def __init__(self,
    chrom, strand, start, end, cds_start, cds_end, ex_count, ex_start, ex_end, hugo):
        self.chrom = chrom
        self.strand = strand
        self.chrom_start = int(start)+1
        self.chrom_end = int(end)
        self.cds_start = int(cds_start)+1
        self.cds_end = int(cds_end)
        
        self.ex_count = int(ex_count)
        self.ex_start = []
        for p in re_comma_end.sub("", ex_start).split(','):
            self.ex_start.append(int(p)+1)
        self.ex_end = []
        for p in re_comma_end.sub("", ex_end).split(','):
            self.ex_end.append(int(p))
        self.name = hugo

    def __repr__(self):
        #return "%s_%s_%d_%d" % (self.hugo, self.chrom,  self.start, self.end )
        return self.name


class RefGene(CGData.CGObjectBase):

    def __init__(self):
        CGData.CGObjectBase.__init__(self)
        self.hugo_map = {}
        self.chrom_map = {}

    def read(self, handle):
        read = csv.reader(handle, delimiter="\t")

        self.hugo_map = {}
        for row in read:
            gene = GeneInfo(
                row[COL_CHROM],
                row[COL_STRAND],
                row[COL_START],
                row[COL_END],
                row[COL_CDSSTART],
                row[COL_CDSEND],
                row[COL_EXCOUNT],
                row[COL_EXSTART],
                row[COL_EXEND],
                row[COL_HUGO])
            if not row[COL_HUGO] in self.hugo_map:
                self.hugo_map[row[COL_HUGO]] = [gene]
            else:
                self.hugo_map[row[COL_HUGO]].append(gene)
        self.chrom_map = {}
        for hugo in self.hugo_map:
            genes = self.hugo_map[hugo]
            for gene in genes:
                if not gene.chrom in self.chrom_map:
                    self.chrom_map[gene.chrom] = []
                self.chrom_map[gene.chrom].append(gene)

        for chrom in self.chrom_map:
            self.chrom_map[chrom].sort(
            lambda x, y: x.chrom_start - y.chrom_start)
        self.loaded = True

    def add(self, gene):
        if gene.chrom not in self.chrom_map:
            self.chrom_map[gene.chrom] = []
        self.chrom_map[gene.chrom].append(gene)
        if gene.name not in self.hugo_map:
            self.hugo_map[gene.name] = []
        self.hugo_map[gene.name].append(gene)
        

    def get_chrom_list(self):
        if not self.loaded:
            self.load()
        return self.chrom_map.keys()

    def has_chrom(self, chrom):
        if not self.loaded:
            self.load()
        return chrom in self.chrom_map

    def get_chrom(self, chrom):
        if not self.loaded:
            self.load()
        return self.chrom_map[chrom]
    
    def get_gene_list(self):
        if not self.loaded:
            self.load()
        return self.hugo_map.keys()
    
    def get_gene(self, gene):
        if not self.loaded:
            self.load()
        return self.hugo_map[gene]