#!/usr/bin/env python
"""exongaplength.py <tiling data> <gap list> <annotation>
Script to compute a list of tiling gap lengths that occur within exons. gap list is a file with a list of two columns --
the begin and end of each gap respectively.
"""
import sys
from common.feature import Features
from common.expressionstruct import Expression
if len(sys.argv) != 4:
print 'Invalid arguments'
print __doc__
sys.exit(0)
features = Features(sys.argv[3])
expression = Expression(sys.argv[1])
header = expression.expression.keys()[0]
(ref, start, end) = header.split(':')[0:3]
startref, endref = int(start), int(end)
exonstring = features.exonString(ref, startref, endref)
gapstring = [0]*(endref - startref + 1)
for line in open(sys.argv[2]):
(gstart, gend) = line.split()[0:2]
gstart, gend = int(gstart), int(gend)
gapstring[gstart-startref:gend-startref] = [1]*(gend-gstart)
for a in range(len(gapstring)):
if not (gapstring[a] and exonstring[a] == 'F'):
#!/usr/bin/env python
"""overlaptransfrag.py <transfrag file>
Takes transfrags from different time points and overlaps them to produce gff"""
import sys
from common.feature import Features, Feature
if len(sys.argv) != 2:
print "Invalid arguments"
print __doc__
sys.exit(0)
startref = 10506243
endref = 13506243
#nucleotide level only...
lines = [line.split() for line in open(sys.argv[1])]
features = Features()
count = 0
for words in lines:
if words:
if words[0] != 'Time':
count += 1
start = int(words[0])
end = int(words[1])
if start > startref and start < endref:
features.addFeature(Feature('Adh', 'manak', ['transfrag'], [[start,end]], None, '+', None, 'Gene ' + str(count)))
features.writeGff(sys.argv[1] + '.out')
