def question_07():
sequences, qualities = dnaseq.read_fastq("ERR037900_1.first1000.fastq")
stats = {}
for i in range(len(sequences)):
for j in range(len(sequences[i])):
stats[j] = stats.get(j, 0) + qualities[i][j]
r = min(stats.iterkeys(), key=(lambda x: stats[x]))
print "question_07: %i" % r
#!/usr/bin/python
import dnaseq
import bm_preproc
import kmer_index
human_chromosome = dnaseq.read_genome("chr1.GRCh38.excerpt.fasta")
phix_reads, _ = dnaseq.read_fastq("ERR266411_1.for_asm.fastq")
def question_01():
p = "GCTGATCGATCGTACG"
d = dnaseq.approximate_match_distance(human_chromosome, p)
print "question_01: %i" % d
def question_02():
p = "GATTTACCAGATTGAG"
d = dnaseq.approximate_match_distance(human_chromosome, p)
print "question_02: %i" % d
def question_03():
d, _ = dnaseq.overlap_graph(phix_reads, 30)
print "question_03: %i" % len(d)
def question_04():
_, n = dnaseq.overlap_graph(phix_reads, 30)
print "question_04: %i" % n
if __name__ == '__main__':
question_01()
question_02()
#!/usr/bin/python
import dnaseq
import bm_preproc
import kmer_index
mystery_virus_reads, _ = dnaseq.read_fastq("ads1_week4_reads.fq")
mystery_virus_genom = dnaseq.assemble(mystery_virus_reads, 30)
def question_01():
ss = ["CCT", "CTT", "TGC", "TGG", "GAT", "ATT"]
s, _ = dnaseq.scs(ss)
print "question_01: %i" % len(s)
def question_02():
ss = ["CCT", "CTT", "TGC", "TGG", "GAT", "ATT"]
_, options = dnaseq.scs(ss)
print "question_02: %i" % len(options)
def question_03():
print "question_03: %i" % mystery_virus_genom.count("A")
def question_04():
print "question_04: %i" % mystery_virus_genom.count("T")
def question_05():
print "question_04:"
print "--------- GENOM BEGIN ---------"
print mystery_virus_genom
print "--------- GENOM END ---------"