basically i read file.txt line by line and the problem is that he reads some invisible symbols. To prove that i try to show length of the string and it's is greater by 1 than real is.
Here is my code:
new_words = []
with open("./file.txt") as f:
new_words = [word.strip() for word in f]
for w in new_words:
print("word: " +str(w) + "length: " + str(len(w)))
And it shows that length is a bigger by 1 that the real length, for example instead of 10 it shows 11.
Well the problem is that there is a hidden symbol. To show it there is a command print([ord(c) for c in w]). To delete it please use the command rstrip(), but this returns new string so w = w.rstrip().
Related
I am using python 2.7.
I want to find the DNA length. I have no idea where is the mistake.....The length of DNA supposed to be 283, but it comes up with 345.
The sequence in a single line is nothing wrong but just the length have some problem.....
I think the spaces are calculated too. May I know how to get the length of the DNA without including the spaces?
Thank you.
import re
singleSeq = ""
fh = open("seq.embl.txt")
lines = fh.readlines()
for line in lines:
lines = line.strip()
m = re.match(r"\s+(.[^\d]+)\s+\d+", line)
if m:
print(m.group(0))
seqline = m.group(1)
print(seqline)
singleSeq += seqline
print("\nSequence in a single line: ")
# print(line.strip(singleSeq))
print(singleSeq)
print("\nSequence length: ", len(singleSeq))
Output
Sequence in a single line:
cccatgtccc agcggcgtat tgctttgcat cgcgaacgca ctttcaatgt cccagcggcg tattgcttct attttataag taccagctaa attttttttt tttttttata agtaccagct aaaatttttt tttttttttt ttataagtac cagctaaaat tttttttttt tttttttata agtaccagct aaaatttttt ttttttttta taagttccag cggcgtattg ctttctgaaa tttaaaaaaa aaaaaaaatt tttttttaat aatatattat ata
Sequence length: 345
This should do the trick
# Python3 code to remove whitespace
def remove(string):
return string.replace(" ", "")
# Driver Program
string = ' t e s t '
print(remove(string))
it seems you are reinventing the wheel her. i strongly suggest you try BioPython for this
from Bio import SeqIO
record = SeqIO.read("seq.embl.txt", "embl")
print("\nSequence length: ", len(record))
In my assignment i'm expected to look for a word and only return a set number of characters (which is 80, and 40 on each side surrounding the word), without the use of nltk or regex.
I've set my code up as so
open = open("a2.txt", 'r')
file2read = open.readlines()
name = 'word'
for line in file2read:
s2 = line.split ("\n", 1)
if name in line:
i = line.find(name)
half = (80 - len(name) - 2) // 2
left = line[i - half]
right = line[i + len(word) + half]
print(left + word + right)
but then my print out looks like this(updated screenshot) instead of the 80 character lines which i'm hoping to find.
Sorry if this is a really newbie error as i'm only 3 weeks into the program and i've been searching and can't seem to get the answer
Instead of doing readlines which might not be consistent due to differences in windows/Unix you can also read the entire text at once:
You don't need to separate it in lines:
with open('a2.txt', 'r') as file:
a = file.read()
name = 'word'
if name in a:
i = a.find(name)
half = (80 - len(name) - 2) // 2
left = a[i-half:i]
right = a[i+len(name):i + len(name) + half]
print(left + name + right)
This way you are reading the entire text at once. Finding your word and printing the necessary 80 characters. This is the output
ut. even know say trip tip sandwich. words describe it. meat eater, love it. b
If you want to make it work for all the words in the text. You will need to make a loop =) but that i'm sure you can figure it out by yourself!
i am very new in python (and programming in general) and here is my issue. i would like to replace (or delete) a part of a string from a txt file which contains hundreds or thousands of lines. each line starts with the very same string which i want to delete.
i have not found a method to delete it so i tried a replace it with empty string but for some reason it doesn't work.
here is what i have written:
file = "C:/Users/experimental/Desktop/testfile siera.txt"
siera_log = open(file)
text_to_replace = "Chart: Bar Backtest: NQU8-CME [CB] 1 Min #1 | Study: free dll = 0 |"
for each_line in siera_log:
new_line = each_line.replace("text_to_replace", " ")
print(new_line)
when i print it to check if it was done, i can see that the lines are as they were before. no change was made.
can anyone help me to find out why?
each line starts with the very same string which i want to delete.
The problem is you're passing a string "text_to_replace" rather than the variable text_to_replace.
But, for this specific problem, you could just remove the first n characters from each line:
text_to_replace = "Chart: Bar Backtest: NQU8-CME [CB] 1 Min #1 | Study: free dll = 0 |"
n = len(text_to_replace)
for each_line in siera_log:
new_line = each_line[n:]
print(new_line)
If you quote a variable it becomes a string literal and won't be evaluated as a variable.
Change your line for replacement to:
new_line = each_line.replace(text_to_replace, " ")
I have a folder with about 50 .txt files containing data in the following format.
=== Predictions on test data ===
inst# actual predicted error distribution (OFTd1_OF_Latency)
1 1:S 2:R + 0.125,*0.875 (73.84)
I need to write a program that combines the following: my index number (i), the letter of the true class (R or S), the letter of the predicted class, and each of the distribution predictions (the decimals less than 1.0).
I would like it to look like the following when finished, but preferably as a .csv file.
ID True Pred S R
1 S R 0.125 0.875
2 R R 0.105 0.895
3 S S 0.945 0.055
. . . . .
. . . . .
. . . . .
n S S 0.900 0.100
I'm a beginner and a bit fuzzy on how to get all of that parsed and then concatenated and appended. Here's what I was thinking, but feel free to suggest another direction if that would be easier.
for i in range(1, n):
s = str(i)
readin = open('mydata/output/output'+s+'out','r')
#The files are all named the same but with different numbers associated
output = open("mydata/summary.csv", "a")
storage = []
for line in readin:
#data extraction/concatenation here
if line.startswith('1'):
id = i
true = # split at the ':' and take the letter after it
pred = # split at the second ':' and take the letter after it
#some have error '+'s and some don't so I'm not exactly sure what to do to get the distributions
ds = # split at the ',' and take the string of 5 digits before it
if pred == 'R':
dr = #skip the character after the comma but take the have characters after
else:
#take the five characters after the comma
lineholder = id+' , '+true+' , '+pred+' , '+ds+' , '+dr
else: continue
output.write(lineholder)
I think using the indexes would be another option, but it might complicate things if the spacing is off in any of the files and I haven't checked this for sure.
Thank you for your help!
Well first of all, if you want to use CSV, you should use CSV module that comes with python. More about this module here: https://docs.python.org/2.7/library/csv.html I won't demonstrate how to use it, because it's pretty simple.
As for reading the input data, here's my suggestion how to break down every line of the data itself. I assume that lines of data in the input file have their values separated by spaces, and each value cannot contain a space:
def process_line(id_, line):
pieces = line.split() # Now we have an array of values
true = pieces[1].split(':')[1] # split at the ':' and take the letter after it
pred = pieces[2].split(':')[1] # split at the second ':' and take the letter after it
if len(pieces) == 6: # There was an error, the + is there
p4 = pieces[4]
else: # There was no '+' only spaces
p4 = pieces[3]
ds = p4.split(',')[0] # split at the ',' and take the string of 5 digits before it
if pred == 'R':
dr = p4.split(',')[0][1:] #skip the character after the comma but take the have??? characters after
else:
dr = p4.split(',')[0]
return id_+' , '+true+' , '+pred+' , '+ds+' , '+dr
What I mainly used here was split function of strings: https://docs.python.org/2/library/stdtypes.html#str.split and in one place this simple syntax of str[1:] to skip the first character of the string (strings are arrays after all, we can use this slicing syntax).
Keep in mind that my function won't handle any errors or lines formated differently than the one you posted as an example. If the values in every line are separated by tabs and not spaces you should replace this line: pieces = line.split() with pieces = line.split('\t').
i think u can separte floats and then combine it with the strings with the help of re module as follows:
import re
file = open('sample.txt','r')
strings=[[num for num in re.findall(r'\d+\.+\d+',i) for i in file.readlines()]]
print (strings)
file.close()
file = open('sample.txt','r')
num=[[num for num in re.findall(r'\w+\:+\w+',i) for i in file.readlines()]]
print (num)
s= num+strings
print s #[['1:S','2:R'],['0.125','0.875','73.84']] output of the code
this prog is written for one line u can use it for multiple line as well but u need to use a loop for that
contents of sample.txt:
1 1:S 2:R + 0.125,*0.875 (73.84)
2 1:S 2:R + 0.15,*0.85 (69.4)
when you run the prog the result will be:
[['1:S,'2:R'],['1:S','2:R'],['0.125','0.875','73.84'],['0.15,'0.85,'69.4']]
simply concatenate them
This uses regular expressions and the CSV module.
import re
import csv
matcher = re.compile(r'[[:blank:]]*1.*:(.).*:(.).* ([^ ]*),[^0-9]?(.*) ')
filenametemplate = 'mydata/output/output%iout'
output = csv.writer(open('mydata/summary.csv', 'w'))
for i in range(1, n):
for line in open(filenametemplate % i):
m = matcher.match(line)
if m:
output.write([i] + list(m.groups()))
I'm trying to write a program that opens a text file, and shifts each of the characters in the file 5 characters to the right. It should only do this for alphanumeric characters, and leave nonalphanumerics as they are. (ex: C becomes H) I'm supposed to be using the ASCII table to do this, and I'm having an issue when the characters wrap around. ex: w should become b, but my program gives me a character that's in the ASCII table. Another issue I'm having is that all the characters are printing on separate lines and I'd like them all to print on the same line.
I can't use lists or dictionaries.
This is what I have, I'm not sure how to do the final if statement
def main():
fileName= input('Please enter the file name: ')
encryptFile(fileName)
def encryptFile(fileName):
f= open(fileName, 'r')
line=1
while line:
line=f.readline()
for char in line:
if char.isalnum():
a=ord(char)
b= a + 5
#if number wraps around, how to correct it
if
print(chr(c))
else:
print(chr(b))
else:
print(char)
Using str.translate:
In [24]: import string
In [25]: string.uppercase
Out[25]: 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
In [26]: string.uppercase[5:]+string.uppercase[:5]
Out[26]: 'FGHIJKLMNOPQRSTUVWXYZABCDE'
In [27]: table = string.maketrans(string.uppercase, string.uppercase[5:]+string.uppercase[:5])
In [28]: 'CAR'.translate(table)
Out[28]: 'HFW'
In [29]: 'HELLO'.translate(table)
Out[29]: 'MJQQT'
First, it matters if it is lower or upper case. I am going to assume here that all the characters are lower case (if they aren't, it would be easy enough to make them)
if b>122:
b=122-b #z=122
c=b+96 #a=97
w=119 in ASCII and z=122 (decimal in ASCII) so 119+5=124 and 124-122=2 which is our new b, then we add that to a-1 (this takes care of if we get a 1 back, 2+96=98 and 98 is b.
For the printing on the same line, instead of printing when you have them, I would write them to a list, then create a string from that list.
e.g instead of
print(chr(c))
else:
print(chr(b))
I would do
someList.append(chr(c))
else:
somList.append(chr(b))
then join each element of the list together into one string.
You could create a dictionary to handle it:
import string
s = string.lowercase + string.uppercase + string.digits + string.lowercase[:5]
encryptionKey = {s[i]:s[i+5] for i in range(len(s)-5)}
The final addend to s (+ string.lowercase[:5]) adds the first 5 letters into the key. Then, we use a simple dictionary comprehension to create a key for the encryption.
Put into your code (I also changed it so you iterate through the lines rather than using f.readline():
import string
def main():
fileName= input('Please enter the file name: ')
encryptFile(fileName)
def encryptFile(fileName):
s = string.lowercase + string.uppercase + string.digits + string.lowercase[:5]
encryptionKey = {s[i]:s[i+5] for i in range(len(s)-5)}
f= open(fileName, 'r')
line=1
for line in f:
for char in line:
if char.isalnum():
print(encryptionKey[char])
else:
print(char)