This is the problem: http://rosalind.info/problems/cons/
def file_read(fname):
with open(fname, "r") as myfile:
global data
data = myfile.readlines()
print(data)
i = 0
while i < len(data):
data[i] = data[i].replace("\n", "")
if ">" in data[i]:
data.remove(data[i])
else:
i += 1
file_read('rosalind_cons.txt')
res = ["".join(el) for el in zip(*data)]
print(res)
a_str = ""
c_str = ""
g_str = ""
t_str = ""
for x in range(0, len(res)):
a_str += (str(res[x].count("A"))) + " "
for x in range(0, len(res)):
c_str += (str(res[x].count("C"))) + " "
for x in range(0, len(res)):
g_str += (str(res[x].count("G"))) + " "
for x in range(0, len(res)):
t_str += (str(res[x].count("T"))) + " "
a_str_nospace = a_str.replace(" ", "")
c_str_nospace = c_str.replace(" ", "")
g_str_nospace = g_str.replace(" ", "")
t_str_nospace = t_str.replace(" ", "")
consensus_string = ""
for x in range(0, len(a_str_nospace)):
if max(a_str_nospace[x], c_str_nospace[x], g_str_nospace[x], t_str_nospace[x]) in a_str_nospace[x]:
consensus_string += "A"
elif max(a_str_nospace[x], c_str_nospace[x], g_str_nospace[x], t_str_nospace[x]) in c_str_nospace[x]:
consensus_string += "C"
elif max(a_str_nospace[x], c_str_nospace[x], g_str_nospace[x], t_str_nospace[x]) in g_str_nospace[x]:
consensus_string += "G"
elif max(a_str_nospace[x], c_str_nospace[x], g_str_nospace[x], t_str_nospace[x]) in t_str_nospace[x]:
consensus_string += "T"
print(consensus_string)
print("A: " + a_str)
print("C: " + c_str)
print("G: " + g_str)
print("T: " + t_str)
What's wrong with my code?
For the sample output it works but for the larger datasets it doesn't.
I don't know what is wrong, I think it's the file reading part that's not correct (maybe?)
EDIT: There are some print functions in there but I don't copy them in the answer box so they don't matter in the result
nice to see a fellow Rosalind user. I discovered that page when I studied Bioinformatics and just stumbled upon it again last month.
To answer your question:
You're creating a string of numbers, so that works fine if the numbers are all below 10.
Try building a list of integers first and only convert them to a string in the final step.
Related
Not allowed to use "Split(),Reverse(),Join() or regexes" or any other
helping inbuilt python function
input something like this:
" my name is scheven "
output like this:
"ym eman si nevehcs"
you need to consider removing the starting,inbetween,ending spaces aswell in the input
I have tried 2 tries, both failed i will share my try to solve this and maby an idea to improve it
First try:
def reverseString(someString):
#lenOfString = len(someString)-1
emptyList = []
for i in range(len(someString)):
emptyList.append(someString[i])
lenOfString = len(emptyList)-1
counter = 0
while counter < lenOfString:
if emptyList[counter] == " ":
counter+=1
if emptyList[lenOfString] == " ":
lenOfString-=1
else:
swappedChar = emptyList[counter]
emptyList[counter] = emptyList[lenOfString]
emptyList[lenOfString] = swappedChar
counter+=1
lenOfString-=1
str_contactantion = ""
#emptyList = emptyList[::-1]
#count_spaces_after_letter=0
for letter in emptyList:
if letter != " ":
str_contactantion+=letter
#str_contactantion+=" "
str_contactantion+=" "
return str_contactantion
second try:
def reverse(array, i, j):
emptyList = []
if (j == i ):
return ""
for k in range(i,j):
emptyList.append(array[k])
start = 0
end = len(emptyList) -1
if start > end: # ensure i <= j
start, end =end, start
while start < end:
emptyList[start], emptyList[end] = emptyList[end], emptyList[start]
start += 1
end -= 1
strconcat=""
for selement in emptyList:
strconcat+=selement
return strconcat
def reverseStr(someStr):
start=0
end=0
help=0
strconcat = ""
empty_list = []
for i in range(len(someStr)):
if(someStr[i] == " "):
continue
else:
start = i
j = start
while someStr[j] != " ":
j+=1
end = j
#if(reverse(someStr,start,end) != ""):
empty_list.append(reverse(someStr,start,end))
empty_list.append(" ")
for selement in empty_list:
strconcat += selement
i = end + 1
return strconcat
print(reverseStr(" my name is scheven "))
The following works without managing indices:
def reverseString(someString):
result = crnt = ""
for c in someString:
if c != " ":
crnt = c + crnt # build the reversed current token
elif crnt: # you only want to do anything for the first space of many
if result:
result += " " # append a space first
result += crnt # append the current token
crnt = "" # and reset it
if crnt:
result += " " + crnt
return result
reverseString(" my name is scheven ")
# 'ym eman si nevehcs'
Try this:
def reverseString(someString):
result = ""
word = ""
for i in (someString + " "):
if i == " ":
if word:
result = result + (result and " ") + word
word = ""
else:
word = i + word
return result
You can then call it like this:
reverseString(" my name is scheven ")
# Output: 'ym eman si nevehcs'
Try this:
string = " my name is scheven "
def reverseString(someString):
result = ''
curr_word = ''
for i in someString:
if i == ' ':
if curr_word:
if result:
result = f'{result} {curr_word}'
else:
result = f'{result}{curr_word}'
curr_word = ''
else:
curr_word = f'{i}{curr_word}'
return result
print(repr(reverseString(string)))
Output:
'ym eman si nevehcs'
Note: if you're allowed to use list.append method, I'd suggest using a collections.deque as it's more performant than appending to a list. But of course, in the end you'll need to join the list together, and you mentioned that you're not allowed to use str.join, so that certainly poses an issue.
I'm making a small program that shoots out math problems and requires an answer to pass. It works fine, but all the randint values I generate stay static for as long as the progran is running. I figured if I change:
Tehtävä = random.choice(Laskut)
Into a function it should refresh with the loop. Problem is I can't for the life of me figure out how to do that. Would it even work for what I'm trying? The randint values are determined in a seperate list. Heres the rest of the code:
Peli = 1
while Peli != 2:
pulma = 1
refresh = 1
Tehtävä = random.choice(Laskut)
while pulma == 1:
ratkaisu = float(input(Tehtävä.problem + "\n:"))
if ratkaisu == Tehtävä.answer:
pulma += 1
refresh += 1
print("oikein")
elif ratkaisu == "loppu":
pulma += 1
refresh += 1
Peli += 1
else:
print("väärin")
Here are the values I used:
import random
class Algebra:
def __init__(self, problem, answer):
self.problem = problem
self.answer = answer
#Muuttujat
#erotus ja summa
a = random.randint(1,99)
b = random.randint(1,99)
c = random.randint(1,99)
d = random.randint(1,99)
#jako ja kerto
e = random.randint(1,10)
f = e*random.randint(1,10)
g = random.randint(1,10)
#Kysymykset
Kysymys_M = [str(a) + "+" + str(b) + "-x=" + str(c),
str(a) + "-" + str(b) + "-x=" + str(a),
str(a) + "-" + str(b) + "-" + str(c) + "-x=" + str(d),
str(e) + "*x=" + str(f),
str(f) + ":x=" + str(e),
"x:" + str(e) + "=" + str(g)]
#Vastaukset
Vastaus_M = [a+b-c,
-b,
a-b-c-d,
f/e,
f/e,
e*g]
Laskut = [
Algebra(Kysymys_M[0], Vastaus_M[0]),
Algebra(Kysymys_M[1], Vastaus_M[1]),
Algebra(Kysymys_M[2], Vastaus_M[2]),
Algebra(Kysymys_M[3], Vastaus_M[3]),
Algebra(Kysymys_M[4], Vastaus_M[4]),
Algebra(Kysymys_M[5], Vastaus_M[5]),]
(If I have packed too much information please let me know.)
I'm having some formatting issues with my call to print function. For lack of knowledge of better ways to format, i've ended up with an issue. here is what it should look like
However the actual result of my print returns this.
def tupleMaker(inputString):
s1 = inputString.split()
# Adding the surname at the end of the string
s2 = [s1[len(s1) - 1]]
# Number of other names(no surname)
global noOfNames
noOfNames = len(s1) - 4
# Adding all the other names
for i in range(noOfNames):
s2.append((s1[i + 3]))
# Adding the Reg number
s2.append(s1[0])
# Adding the Degree scheme
s2.append(s1[2])
# Adding the year
s2.append("Year " + s1[1])
# Making it a tuple
t = ()
for i in range(len(s2)):
t = t + (s2[i],)
return t
def formatting(t):
s1 = ""
for i in range(len(t)):
s1 += t[i]
if (i == 0):
s1 += ", "
elif (i == len(t) - 4):
s1 += " "
else:
s1 += " "
#print(t[0] + ", ", end="")
#for i in range(noOfNames):
#print (t[i+1], end= " ")
#print(format(t[1+noOfNames], "<32s"))
#print(format(thenames, "<32d") + format(regNo, "<7d") + format(degScheme, ">6s") + format(year, ">1s")
print("")
print(s1)
I would recommend looking at using pythons built in string.format() function a small tutorial is located here: https://pyformat.info/
import sys
import string
import re
keywords = []
task = "*"
while task not in "ed":
task = raw_input("Encrypt or Decrypt: \nType ‘e’ to Encrypt\nType ‘d’ to Decrypt\n").lower()
keyword = "*"
keyphrase = "*"
while not(re.match('[a-z ]+$',keyword)):
keyword = raw_input("enter your first keyword:-").lower()
while not(re.match('[a-z ]+$',keyphrase)):
keyphrase = raw_input("enter a key phrase:-").lower()
loop = 0
repeated_keyword = ""
if len(keyword) < len(keyphrase):
while len(repeated_keyword) < len(keyphrase):
repeated_keyword = repeated_keyword + keyword[loop]
loop += 1
if loop >= len(keyword):
loop = 0
elif len(keyword) == len(keyphrase):
repeated_keyword = keyword
last_charecter_in_keyword = keyword[-1]
elif len(keyword) > len(keyphrase):
repeated_keyword = keyword
last_charecter_in_keyword = keyword[-1]
while len(repeated_keyword) > len(keyphrase):
repeated_keyword = repeated_keyword[:-1]
repeated_keyword_letter_positions = []
keyphrase_letter_positions = []
for character in repeated_keyword:
position_of_char_in_repeated_keyword = (string.ascii_lowercase + " ").find(character) +1
repeated_keyword_letter_positions.append(position_of_char_in_repeated_keyword)
for character in keyphrase:
position_of_char_in_keyphrase = (string.ascii_lowercase + " ").find(character)
keyphrase_letter_positions.append(position_of_char_in_keyphrase)
if task == "e":
final_positions_of_letters = [a + b for a, b in zip(keyphrase_letter_positions,repeated_keyword_letter_positions)]
elif task == "d":
final_positions_of_letters = [a - b for a, b in zip(keyphrase_letter_positions,repeated_keyword_letter_positions)]
new_letter = ""
final_cipher = []
loop = 0
alphabet = string.ascii_lowercase + " " + string.ascii_lowercase + " "
while loop < len(final_positions_of_letters):
new_letter =alphabet[final_positions_of_letters[loop]]
final_cipher = str(final_cipher) + str(new_letter)
loop += 1
print final_cipher
This is a encryption/ decryption programme in python 2.7. However at the end of the programme when the final_cipher list is printed to the shell a pair of [] brackets are printed prior to the contents of the list
You have some options here:
• Loop through the array, and print each element on the same row without delimiter.
• Use 'join' to join all the parts of the array in a single string. You can find more information about the join statement here.
Personally I do think 'join' is the best option here.
I guess you are trying to output a string. And you are making a mistake by setting the initial declaration to an empty list.
For fixing this just use :
final_cipher = "" instead of final_cipher = []
This should get you the output in string format.
Seeing:
final_cipher = []
loop = 0
alphabet = string.ascii_lowercase + " " + string.ascii_lowercase + " "
while loop < len(final_positions_of_letters):
new_letter =alphabet[final_positions_of_letters[loop]]
final_cipher = str(final_cipher) + str(new_letter)
loop += 1
print final_cipher
I see that you are working with final_cipher like a string, then you should initialize like:
final_cipher = ""
And:
final_cipher = str(final_cipher) + str(new_letter)
Should be:
final_cipher = final_cipher + str(new_letter)
Or better:
final_cipher += str(new_letter)
final_cipher is a list, so yes, printing it will print it as a string, i.e. the result of calling str(final_cipher).
If you want to just print the elements seperated by a comma, you can use .join:
print ", ".join(final_cipher)
You create final_cipher as a list but then change your mind and do string concatenation instead. On the first iteration of the loop, str(final_cipher) creates the string representation of an empty list "[]". Look familiar? Keep a list and build the string at the end.
final_cipher = []
loop = 0
alphabet = string.ascii_lowercase + " " + string.ascii_lowercase + " "
while loop < len(final_positions_of_letters):
new_letter =alphabet[final_positions_of_letters[loop]]
final_cipher.append(str(new_letter))
loop += 1
final_cipher = ''.join(final_cipher)
print final_cipher
I am fairly new to python, I am not sure on how to fix a index string out of range. it happens right after the while loop when I want to send mylist[i][0] to formatting function. Any pointer on my code in general would be awesome!
def formatting(str1):
if str1 == '?':
return True
else:
return False
while(i <= len(mylist)):
val = formatting(mylist[i][0])
if val == True:
str1 = mylist[i]
str2 = mylist[i+1]
i = i + 2
format_set(str1, str2)
else:
if format == True:
if (margin + count + len(mylist[i])) <= width:
if (i == (len(mylist)-1)):
list2.append(mylist[i])
print(" " * margin + " ".join(list2))
break
list2.append(mylist[i])
count += len(mylist[i])
i += 1
else:
print(" " * margin + " ".join(list2))
list2 = []
count = 0
else:
temp_margin = margin
temp_width = width
width = 60
margin = 0
if (margin + count + len(mylist[i])) <= width:
if (i == (len(mylist)-1)):
list2.append(mylist[i])
print(" " * margin + " ".join(list2))
margin = temp_margin
width = temp_width
break
list2.append(mylist[i])
count += len(mylist[i])
i += 1
else:
print(" " * margin + " ".join(list2))
list2 = []
count = 0
change
i <= len(mylist)
to
i < len(mylist)
In the last iteration of the while loop, i is referring to the last value. Hence,
str2 = mylist[i+1]
is trying to reference a string outside the allowed range and you get an error.
EDIT: Also, as Wcrousse mentioned, the while (i <= len(...)) should be changed to i < len(...) because indexes go from 0 - (length-1).