def main():
# question 1: What is the length of the shortest common superstring of the following strings?
shortest_string, num_strings = utils.scs(['CCT', 'CTT', 'TGC', 'TGG', 'GAT', 'ATT'])
print len(shortest_string)
# question 2: How many different shortest common superstrings are there for the input strings given in the previous question?
print num_strings
# question 3 and 4:
unknown_virus_seq, _ = utils.readFastq('ads1_week4_reads.fq')
for k in range(100, 1, -1):
genome = utils.greedy_scs(unknown_virus_seq, k)
if len(genome) == 15894:
# q3: How many As are there in the full, assembled genome?
print(genome.count('A'))
# q4: How many As are there in the full, assembled genome?
print(genome.count('T'))
# g5: final genome that we can search for in the BLAST database
print(genome)
break
def main():
chr1 = utils.readGenome('chr1.GRCh38.excerpt.fasta')
#Question 1
start = time.clock()
print edit_distance_alt('GCTGATCGATCGTACG', chr1)
end = time.clock()
print ">> %.2gs" % (end - start)
#Question 2
start = time.clock()
print edit_distance_alt('GATTTACCAGATTGAG', chr1)
end = time.clock()
print ">> %.2gs" % (end - start)
#Questions 3 and 4
start = time.clock()
seqs, _ = utils.readFastq('ERR266411_1.for_asm.fastq')
edges, suffixes = overlap_graph(seqs, 30)
print edges
print suffixes
end = time.clock()
print ">> %.2gs" % (end - start)
def main():
chr1 = utils.readGenome("chr1.GRCh38.excerpt.fasta")
# Question 1
start = time.clock()
print edit_distance_alt("GCTGATCGATCGTACG", chr1)
end = time.clock()
print ">> %.2gs" % (end - start)
# Question 2
start = time.clock()
print edit_distance_alt("GATTTACCAGATTGAG", chr1)
end = time.clock()
print ">> %.2gs" % (end - start)
# Questions 3 and 4
start = time.clock()
seqs, _ = utils.readFastq("ERR266411_1.for_asm.fastq")
edges, suffixes = overlap_graph(seqs, 30)
print edges
print suffixes
end = time.clock()
print ">> %.2gs" % (end - start)
def main():
# question 1: What is the length of the shortest common superstring of the following strings?
shortest_string, num_strings = utils.scs(
['CCT', 'CTT', 'TGC', 'TGG', 'GAT', 'ATT'])
print len(shortest_string)
# question 2: How many different shortest common superstrings are there for the input strings given in the previous question?
print num_strings
# question 3 and 4:
unknown_virus_seq, _ = utils.readFastq('ads1_week4_reads.fq')
for k in range(100, 1, -1):
genome = utils.greedy_scs(unknown_virus_seq, k)
if len(genome) == 15894:
# q3: How many As are there in the full, assembled genome?
print(genome.count('A'))
# q4: How many As are there in the full, assembled genome?
print(genome.count('T'))
# g5: final genome that we can search for in the BLAST database
print(genome)
break
from utils import readFastq
from w4 import scs
seq, _ = readFastq('ads1_week4_reads.fq')
combined = scs(seq)
print(len(combined))
print(combined.count('A'))
print(combined.count('T'))
