Entrez.email = "*****@*****.**"
if __name__ == "__main__":
with open('rosalind_need.txt') as dataset:
ids = dataset.read().split()
handle = Entrez.efetch(db='nucleotide', id=ids, rettype="fasta")
records = list(SeqIO.parse(handle, 'fasta'))
for i, r in enumerate(records):
with open(ids[i], 'w') as f:
SeqIO.write(r, f, 'fasta')
needle_cline = NeedleCommandline()
needle_cline.asequence = ids[0]
needle_cline.bsequence = ids[1]
needle_cline.outfile = "rosalind_need_output.txt"
needle_cline.gapopen = 10
needle_cline.gapextend = 1
needle_cline.endopen = 10
needle_cline.endextend = 1
needle_cline.endweight = True
needle_cline()
with open('rosalind_need_output.txt') as f:
output = f.readlines()
for line in output:
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
if __name__ == "__main__":
with open(os.path.join('data', 'rosalind_need.txt')) as dataset:
ids = dataset.read().split()
handle = Entrez.efetch(db='nucleotide', id=ids, rettype="fasta")
records = list(SeqIO.parse(handle, 'fasta'))
for i, r in enumerate(records):
with open(ids[i], 'w') as f:
SeqIO.write(r, f, 'fasta')
needle_cline = NeedleCommandline()
needle_cline.asequence = ids[0]
needle_cline.bsequence = ids[1]
needle_cline.outfile = "need.txt"
needle_cline.gapopen = 11
needle_cline.gapextend = 1
needle_cline.endopen = 11
needle_cline.endextend = 1
needle_cline.endweight = True
needle_cline()
with open('need.txt') as f:
output = f.readlines()
for line in output:
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
records = list(SeqIO.parse(handle, 'fasta'))
for i, record in enumerate(records):
with open(ids[i], 'w') as f:
SeqIO.write(record, f, 'fasta')
# Following step can be done in command line
# using 'needle'
needle_cl = NeedleCommandline()
needle_cl.asequence = ids[0]
needle_cl.bsequence = ids[1]
needle_cl.outfile = 'need_output.txt'
needle_cl.gapopen = 10
needle_cl.gapextend = 1
needle_cl.endopen = 10
needle_cl.endextend = 1
needle_cl.endweight = True
needle_cl()
# Score
with open('need_output.txt', 'r') as f:
content = f.readlines()
for line in content:
if 'Score' in line:
score = float(line.split()[-1])
print(score)
break