#!/usr/bin/python
from pyfasta import Fasta
import numpy as np
import sys
fa = Fasta(sys.argv[1]) # softmasked sequence
for seqid, aseq in fa.iteritems():
aseq = np.array(str(aseq).upper(), dtype="c")
print ">%s\n%s" % (seqid, aseq.tostring())
a[start] = a[start - 1]
else:
a[start:end] = (a[start - 1] + a[end]) / 2
if __name__ == "__main__":
import doctest
doctest.testmod()
if __name__ == "__main__":
plookups = parse_posns(posns)
fasta = Fasta("/opt/src/flatfeature/data/thaliana_v9.fasta")
arrs = {}
counts = {}
for seqid, seq in fasta.iteritems():
arrs[seqid] = np.zeros((len(seq),), dtype=np.float32)
counts[seqid] = np.zeros((len(seq),), dtype=np.float32)
print arrs.keys()
success = 0
for id, val in parse_hists(hists):
start, length = plookups[id]
assert val != 0
#print id, val, start, length
seqid = id[3]
if not seqid in "12345": continue
a = arrs[seqid][start - 1: start + length]
counts[seqid][start - 1: start + length] += 1
c = counts[seqid][start -1: start + length]
