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Gene Bed Class
Download gene annotation table from table browser of UCSC genome Browser
Should be Name as GenePred

src/x/p/xplib-0.01/lib/xplib/Tools/__init__.py   xplib(Download)
# Programmer : zhuxp
# Date:  Sep 2012
# Last-modified: 12-04-2013, 17:19:36 EST
from string import upper,lower
from xplib.Annotation import Fragment,Bed,Bed12,GeneBed
        C1=Bed12(bed.toBedString())
        C2=translate_coordinates(coord,C1)
        return GeneBed(C2.toGenePredString())
    else:
        C=copy.copy(bed)

src/x/p/xplib-0.01/lib/xplib/TableIO/GeneBedIO.py   xplib(Download)
# Programmer : zhuxp
# Date: 
# Last-modified: 03 Oct 2012 16:49:30
from xplib.Annotation import GeneBed
import types
def GeneBedIterator(handle,**kwargs):
    '''
    '''
    for x in SimpleIO.SimpleIterator(handle,**kwargs):
        b=GeneBed(x)

src/x/p/xplib-0.01/lib/xplib/TableIO/gtfIO.py   xplib(Download)
        print gene
'''
from xplib.Annotation import GeneBed
import SimpleIO
import sys, re, string, types, copy
    for g in header:
        x.append(GeneTab_line[g])
    gene = GeneBed(x)
    return gene
 

src/x/p/xplib-0.01/bin/xCmpGene.py   xplib(Download)
VERSION="0.1"
import os,sys,argparse
from xplib.Annotation import Bed,Bed12,GeneBed
from xplib import TableIO,Tools
from xplib import DBI