def main():
global pileup
reference = read_fa_file("data/reference.fa")
reads = read_fa_file("data/reads.fa")
# initialize object
am = ApproximateMatcher(reference)
pileup = PileUp(reference)
d = 3
for read in reads:
# find matching positions for a given read
# assumes positions is a list (even if only a single match is found)
# with matching positions
positions = am.get_matches(read, d)
if len(positions) > 0:
# add to pileup object
pileup.insert(positions, read)
# prints out mismatching positions
# output is:
# (<position>, <reference_character>, [(<variant_character>,
# <num_times_aligned>)])
# argument filters mismatch by frequency in which variant character
# is observe, e.g., .01 means variant character has to be seen at least
# once for every 100 aligned nucleotides
pileup.print_mismatches(.01)
def main(filename):
text, patterns, d = readdat(filename)
# initialize approximate matcher
am = ApproximateMatcher(text)
# find approximate matches for each pattern
indices = []
for pattern in patterns:
indices += am.get_matches(pattern, d)
print ' '.join(map(str, sorted(indices)))
def main(filename):
text, patterns, d = readdat(filename)
# initialize approximate matcher
am = ApproximateMatcher(text)
# find approximate matches for each pattern
indices = []
for pattern in patterns:
if not debug:
indices += am.get_matches(pattern, d)
else:
indices += am._bwt.get_matches(pattern)
print ' '.join(map(str, sorted(indices)))
from pileup import PileUp
from approximate_matcher import ApproximateMatcher
import sys
# import the fasta files
f = open(sys.argv[1], 'r')
g = open(sys.argv[2], 'r')
reference = ""
for line in f:
reference += line.rstrip()
reads = (g.readline()).rstrip().split()
reference.rstrip()
print reference[822:835]
# initialize object
am = ApproximateMatcher(reference)
pileup = PileUp(reference)
d = 3
for read in reads:
# find matching positions for a given read
# assumes positions is a list (even if only a single match is found)
# with matching positions
positions = am.get_matches(read, d)
if len(positions) > 0:
# add to pileup object
pileup.insert(positions, read)
# prints out mismatching positions
# output is:
# (<position>, <reference_character>, [(<variant_character>,