def figpath(filename = 'plot.pdf', delete = False):
called_name = inspect.stack()[1][3]
stack = inspect.stack()[1]
call_path = os.path.abspath(stack[1])
path = cfg.relPath(call_path)
figpath = cfg.dataPath(os.path.join('figs',path,called_name,filename))
if delete:
if os.path.isfile(figpath):
os.remove(figpath)
return figpath
def save(self):
savepath = cfg.dataPath('figs/tmp/tmp_fig_{0}.pdf').format(self.num)
self.f.savefig(savepath)
import everySNAKE.config as cfg, everySNAKE.utils.memo as mem
import track
from numpy import *
import os
import numpy as np
#bedfile storing annotations (genes, promoters...)
bedfile = cfg.dataPath('silvana/mouse_genes.bed')
#peakfile storing dnase narrowpeaks.
peakfile = cfg.dataPath('silvana/dhs.narrowPeak')
def getTrackChrPromoters(**kwargs):
'''
Get all of the forward promoter from a bed file
on a given chromosome.
kwargs
num: chromosome number
fname: bedfile path (uses global bedfile as the default)
returns
a list of the coordinates of each forward promoter.
'''
def setTrackChrPromoters(**kwargs):
fname = kwargs.get('fname', bedfile)
num = kwargs.get('num', 1)
t = track.load(fname);
chromosome_data = t.read('chr{0}'.format(num))
rows = [dict(zip(r.keys(),r.data)) for r in iter(chromosome_data)]
fwd_genes = [e for e in rows if e['strand'] == 1]