"""
A very, very basic genome browser.
usage : ./basic_browser.py forward.track \
reverse.track \
peak.bookmark \
genes.bed
"""
import numpy
import pique
import pylab
import sys
# read track data
pique.msg( 'reading track data...' )
data_ff = pique.readtrack( sys.argv[1] )
data_rr = pique.readtrack( sys.argv[2] )
# read peak data
pique.msg( 'reading peak bookmarks...' )
peaks = pique.readbookmarks( sys.argv[3] )
# draw peaks
pique.msg( 'drawing peak bookmarks...' )
for peak in peaks :
axvspan( peak['start'], peak['stop'], color='green', alpha=0.3 )
# read BED formatted gene annotations
pique.msg( 'reading gene annotations...' )
genes = {}
for line in open( sys.argv[4] ) :
'peak_bookmarks', \
'weed_bookmarks', \
'overlap_track', \
'binding_track' ]
opt_dict = yaml.load( open( sys.argv[1] ).read() )
for opt in num_opts + str_opts :
if not opt_dict.has_key( opt ) :
print 'config file missing option : ' + opt
quit()
setattr( sys.modules[__name__], opt, opt_dict[opt] )
# read the track data
pique.msg( 'reading track data...' )
data_ff = pique.readtrack( forward_ChIP_track )
data_rr = pique.readtrack( reverse_ChIP_track )
b_ff = pique.readtrack( forward_bgnd_track )
b_rr = pique.readtrack( reverse_bgnd_track )
# apply mask
pique.msg( 'applying mask...' )
is_elements = []
for line in open( masking_loci ) :
if line.__contains__('#') :
continue
start, stop = map( int, line.split()[:2] )
is_elements.append( { 'start':start, 'stop':stop } )
data_ff = pique.mask( data_ff, is_elements )
data_rr = pique.mask( data_rr, is_elements )
'reverse_ChIP_track', \
'reverse_bgnd_track', \
'masking_loci', \
'annotated_bookmarks' ]
opt_dict = yaml.load(open(sys.argv[1]).read())
for opt in str_opts:
if not opt_dict.has_key(opt):
print 'config file missing option : ' + opt
quit()
setattr(sys.modules[__name__], opt, opt_dict[opt])
# read track data
pique.msg('reading track data...')
data_ff = pique.readtrack(forward_ChIP_track)
data_rr = pique.readtrack(reverse_ChIP_track)
b_ff = pique.readtrack(forward_bgnd_track)
b_rr = pique.readtrack(reverse_bgnd_track)
# read bookmarks file
peaks = pique.readbookmarks(peak_bookmarks)
# calculate enrichment ratios
for n, peak in enumerate(peaks):
a = sum(data_ff[peak['start']:peak['stop']])
a = a + sum(data_rr[peak['start']:peak['stop']])
b = sum(b_ff[peak['start']:peak['stop']])
b = b + sum(b_rr[peak['start']:peak['stop']])
peaks[n]['annotations']['enrichment_ratio'] = float(a) / float(b)
"""
A very, very basic genome browser.
usage : ./basic_browser.py forward.track \
reverse.track \
peak.bookmark \
genes.bed
"""
import numpy
import pique
import pylab
import sys
# read track data
pique.msg('reading track data...')
data_ff = pique.readtrack(sys.argv[1])
data_rr = pique.readtrack(sys.argv[2])
# read peak data
pique.msg('reading peak bookmarks...')
peaks = pique.readbookmarks(sys.argv[3])
# draw peaks
pique.msg('drawing peak bookmarks...')
for peak in peaks:
axvspan(peak['start'], peak['stop'], color='green', alpha=0.3)
# read BED formatted gene annotations
pique.msg('reading gene annotations...')
genes = {}
for line in open(sys.argv[4]):