diff seg2matrix/CGData/RefGene.py @ 31:ab20c0d04f4a

add seg2matrix tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg2matrix/CGData/RefGene.py	Fri Jul 24 13:10:11 2015 -0700
@@ -0,0 +1,124 @@
+
+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]