def readinput( path ):
"""
Read all the segments from FASTA file. Return Fasta object.
"""
fasta = Fasta( path )
for i in range( len(fasta.get_segments()) ):
seg = fasta.get_segments()[i]
seq = seg.get_sequence()
print( seg.get_header() + "\n" + seq )
return fasta
def execute():
fasta = Fasta( "rosalind_tran.txt" )
s1 = fasta.get_segments()[0].get_sequence().upper()
s2 = fasta.get_segments()[1].get_sequence().upper()
print( "s1",s1 )
print( "s2",s2)
ratio = compute_ratio( s1, s2 )
print( "ratio=" + str(ratio) )
def readinput( path ):
"""
Read input from FASTA file.
"""
fasta = Fasta( path )
segs = fasta.get_segments()
s = segs[0].get_sequence()
t = segs[1].get_sequence()
return s,t
def execute():
fasta = Fasta( "rosalind_revp.txt" )
output = open( "output_revp.txt", "w" )
dna = fasta.get_segments()[0].get_sequence()
#print( dna )
restrictions = find_restrictions( dna )
for i in range(len(restrictions)):
print( str(restrictions[i][0])+" "+str(restrictions[i][1]))
output.write(str(restrictions[i][0])+" "+str(restrictions[i][1]))
output.write("\n")
def execute():
"""
text_file = open( "rosalind_hamm.txt", "r")
s = text_file.readline().rstrip()
t = text_file.readline().rstrip()
text_file.close()
"""
from fasta import Fasta
fasta = Fasta( "rosalind_tran.txt" )
s = fasta.get_segments()[0].get_sequence().upper()
t = fasta.get_segments()[1].get_sequence().upper()
if len(s) != len(t):
raise Exception( "lengths do not match" )
print( hamm_dist(s,t) )
def readinput(path):
fasta = Fasta(path)
seq = fasta.get_segments()[0].get_sequence()
return seq