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))
Related
I met some problems about try to use string in text.
here is a provided file sqroot2_10kdigits.txt.
the sqroot2_10kdigits.txt is below:
1.4142135623 7309504880 1688724209 6980785696 7187537694 8073176679 7379907324 7846210703 8850387534 3276415727 3501384623 0912297024
9248360558 5073721264 4121497099 9358314132 2266592750 5592755799
9505011527 8206057147 0109559971 6059702745 3459686201 4728517418
6408891986 0955232923 0484308714 3214508397 6260362799 5251407989
6872533965 4633180882 9640620615 2583523950 5474575028 7759961729
8355752203 3753185701 1354374603 4084988471
My code is below:
myfile = open("sqroot2_10kdigits.txt")
txt = myfile.read()
print(txt)
myfile.close()
Q2: Make a new empty string called sqroot_2_string. Note that there's a space between every 10 digits.Instead of using the .rstrip() method, try using .replace(" ", "") to remove all the spaces in the file and save it in the empty string I just made. Check the length of the string as well, it should be 10002. Then print the first 10 digits followed by .... Here's an example:
The first 10 digit of square root of 2 is 1.4142135623... My codes are below:
def sqroot_2_string(string):
count = 0
list = []
for i in xrange(len(string)):
if string[i] != ' ':
list.append(string[i])
return toString(list)
# Utility Function
def toString(List):
return ''.join(List)
# Driver program
string = myfile
print sqroot_2_string(string)
Anyone can check my code in Q2? I don't know how to use .replace(" ", "") to remove all the spaces in the file and save it in the empty string
You can just do
def sqroot_2_string(string):
return string.replace(" ", "")
Also note that you should do
print(sqroot_2_string(txt))
so you are using the text from the file instead of the file handle
I am surprising, I am using python to slice a long DNA Sequence (4699673 character)to a specific length supstring, it's working properly with a problem in result, after 71 good result \n start apear in result for few slices then correct slices again and so on for whole long file
the code:
import sys
filename = open("out_filePU.txt",'w')
sys.stdout = filename
my_file = open("GCF_000005845.2_ASM584v2_genomic_edited.fna")
st = my_file.read()
length = len(st)
print ( 'Sequence Length is, :' ,length)
for i in range(0,len(st[:-9])):
print(st[i:i+9], i)
figure shows the error from the result file
please i need advice on that.
Your sequence file contains multiple lines, and at the end of each line there is a line break \n. You can remove them with st = my_file.read().replace("\n", "").
Try st = re.sub('\\s', '', my_file.read()) to replace any newlines or other whitespace (you'll need to add import re at the top of your script).
Then for i in range(0,len(st[:-9]),9): to step through your data in increments of nine characters. Otherwise you're only advancing by one character each time: that's why you can see the diagonal patterns in your output.
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().
I'm a python learner. If I have a lines of text in a file that looks like this
"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"
Can I split the lines around the inverted commas? The only constant would be their position in the file relative to the data lines themselves. The data lines could range from 10 to 100+ characters (they'll be nested network folders). I cannot see how I can use any other way to do those markers to split on, but my lack of python knowledge is making this difficult.
I've tried
optfile=line.split("")
and other variations but keep getting valueerror: empty seperator. I can see why it's saying that, I just don't know how to change it. Any help is, as always very appreciated.
Many thanks
You must escape the ":
input.split("\"")
results in
['\n',
'Y:\\DATA\x0001\\SERVER\\DATA.TXT',
' ',
'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT',
'\n']
To drop the resulting empty lines:
[line for line in [line.strip() for line in input.split("\"")] if line]
results in
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
I'll just add that if you were dealing with lines that look like they could be command line parameters, then you could possibly take advantage of the shlex module:
import shlex
with open('somefile') as fin:
for line in fin:
print shlex.split(line)
Would give:
['Y:\\DATA\\00001\\SERVER\\DATA.TXT', 'V:\\DATA2\\00002\\SERVER2\\DATA2.TXT']
No regex, no split, just use csv.reader
import csv
sample_line = '10.0.0.1 foo "24/Sep/2015:01:08:16 +0800" www.google.com "GET /" -'
def main():
for l in csv.reader([sample_line], delimiter=' ', quotechar='"'):
print l
The output is
['10.0.0.1', 'foo', '24/Sep/2015:01:08:16 +0800', 'www.google.com', 'GET /', '-']
shlex module can help you.
import shlex
my_string = '"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
shlex.split(my_string)
This will spit
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
Reference: https://docs.python.org/2/library/shlex.html
Finding all regular expression matches will do it:
input=r'"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
re.findall('".+?"', # or '"[^"]+"', input)
This will return the list of file names:
["Y:\DATA\00001\SERVER\DATA.TXT", "V:\DATA2\00002\SERVER2\DATA2.TXT"]
To get the file name without quotes use:
[f[1:-1] for f in re.findall('".+?"', input)]
or use re.finditer:
[f.group(1) for f in re.finditer('"(.+?)"', input)]
The following code splits the line at each occurrence of the inverted comma character (") and removes empty strings and those consisting only of whitespace.
[s for s in line.split('"') if s.strip() != '']
There is no need to use regular expressions, an escape character, some module or assume a certain number of whitespace characters between the paths.
Test:
line = r'"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
output = [s for s in line.split('"') if s.strip() != '']
print(output)
>>> ['Y:\\DATA\\00001\\SERVER\\DATA.TXT', 'V:\\DATA2\\00002\\SERVER2\\DATA2.TXT']
I think what you want is to extract the filepaths, which are separated by spaces. That is you want to split the line about items contained within quotations. I.e with a line
"FILE PATH" "FILE PATH 2"
You want
["FILE PATH","FILE PATH 2"]
In which case:
import re
with open('file.txt') as f:
for line in f:
print(re.split(r'(?<=")\s(?=")',line))
With file.txt:
"Y:\DATA\00001\SERVER\DATA MINER.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"
Outputs:
>>>
['"Y:\\DATA\\00001\\SERVER\\DATA MINER.TXT"', '"V:\\DATA2\\00002\\SERVER2\\DATA2.TXT"']
This was my solution. It parses most sane input exactly the same as if it was passed into the command line directly.
import re
def simpleParse(input_):
def reduce_(quotes):
return '' if quotes.group(0) == '"' else '"'
rex = r'("[^"]*"(?:\s|$)|[^\s]+)'
return [re.sub(r'"{1,2}',reduce_,z.strip()) for z in re.findall(rex,input_)]
Use case: Collecting a bunch of single shot scripts into a utility launcher without having to redo command input much.
Edit:
Got OCD about the stupid way that the command line handles crappy quoting and wrote the below:
import re
tokens = list()
reading = False
qc = 0
lq = 0
begin = 0
for z in range(len(trial)):
char = trial[z]
if re.match(r'[^\s]', char):
if not reading:
reading = True
begin = z
if re.match(r'"', char):
begin = z
qc = 1
else:
begin = z - 1
qc = 0
lc = begin
else:
if re.match(r'"', char):
qc = qc + 1
lq = z
elif reading and qc % 2 == 0:
reading = False
if lq == z - 1:
tokens.append(trial[begin + 1: z - 1])
else:
tokens.append(trial[begin + 1: z])
if reading:
tokens.append(trial[begin + 1: len(trial) ])
tokens = [re.sub(r'"{1,2}',lambda y:'' if y.group(0) == '"' else '"', z) for z in tokens]
I know this got answered a million year ago, but this works too:
input = '"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
input = input.replace('" "','"').split('"')[1:-1]
Should output it as a list containing:
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
My question Python - Error Caused by Space in argv Arument was marked as a duplicate of this one. We have a number of Python books doing back to Python 2.3. The oldest referred to using a list for argv, but with no example, so I changed things to:-
repoCmd = ['Purchaser.py', 'task', repoTask, LastDataPath]
SWCore.main(repoCmd)
and in SWCore to:-
sys.argv = args
The shlex module worked but I prefer this.
I'm a python learner. If I have a lines of text in a file that looks like this
"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"
Can I split the lines around the inverted commas? The only constant would be their position in the file relative to the data lines themselves. The data lines could range from 10 to 100+ characters (they'll be nested network folders). I cannot see how I can use any other way to do those markers to split on, but my lack of python knowledge is making this difficult.
I've tried
optfile=line.split("")
and other variations but keep getting valueerror: empty seperator. I can see why it's saying that, I just don't know how to change it. Any help is, as always very appreciated.
Many thanks
You must escape the ":
input.split("\"")
results in
['\n',
'Y:\\DATA\x0001\\SERVER\\DATA.TXT',
' ',
'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT',
'\n']
To drop the resulting empty lines:
[line for line in [line.strip() for line in input.split("\"")] if line]
results in
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
I'll just add that if you were dealing with lines that look like they could be command line parameters, then you could possibly take advantage of the shlex module:
import shlex
with open('somefile') as fin:
for line in fin:
print shlex.split(line)
Would give:
['Y:\\DATA\\00001\\SERVER\\DATA.TXT', 'V:\\DATA2\\00002\\SERVER2\\DATA2.TXT']
No regex, no split, just use csv.reader
import csv
sample_line = '10.0.0.1 foo "24/Sep/2015:01:08:16 +0800" www.google.com "GET /" -'
def main():
for l in csv.reader([sample_line], delimiter=' ', quotechar='"'):
print l
The output is
['10.0.0.1', 'foo', '24/Sep/2015:01:08:16 +0800', 'www.google.com', 'GET /', '-']
shlex module can help you.
import shlex
my_string = '"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
shlex.split(my_string)
This will spit
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
Reference: https://docs.python.org/2/library/shlex.html
Finding all regular expression matches will do it:
input=r'"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
re.findall('".+?"', # or '"[^"]+"', input)
This will return the list of file names:
["Y:\DATA\00001\SERVER\DATA.TXT", "V:\DATA2\00002\SERVER2\DATA2.TXT"]
To get the file name without quotes use:
[f[1:-1] for f in re.findall('".+?"', input)]
or use re.finditer:
[f.group(1) for f in re.finditer('"(.+?)"', input)]
The following code splits the line at each occurrence of the inverted comma character (") and removes empty strings and those consisting only of whitespace.
[s for s in line.split('"') if s.strip() != '']
There is no need to use regular expressions, an escape character, some module or assume a certain number of whitespace characters between the paths.
Test:
line = r'"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
output = [s for s in line.split('"') if s.strip() != '']
print(output)
>>> ['Y:\\DATA\\00001\\SERVER\\DATA.TXT', 'V:\\DATA2\\00002\\SERVER2\\DATA2.TXT']
I think what you want is to extract the filepaths, which are separated by spaces. That is you want to split the line about items contained within quotations. I.e with a line
"FILE PATH" "FILE PATH 2"
You want
["FILE PATH","FILE PATH 2"]
In which case:
import re
with open('file.txt') as f:
for line in f:
print(re.split(r'(?<=")\s(?=")',line))
With file.txt:
"Y:\DATA\00001\SERVER\DATA MINER.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"
Outputs:
>>>
['"Y:\\DATA\\00001\\SERVER\\DATA MINER.TXT"', '"V:\\DATA2\\00002\\SERVER2\\DATA2.TXT"']
This was my solution. It parses most sane input exactly the same as if it was passed into the command line directly.
import re
def simpleParse(input_):
def reduce_(quotes):
return '' if quotes.group(0) == '"' else '"'
rex = r'("[^"]*"(?:\s|$)|[^\s]+)'
return [re.sub(r'"{1,2}',reduce_,z.strip()) for z in re.findall(rex,input_)]
Use case: Collecting a bunch of single shot scripts into a utility launcher without having to redo command input much.
Edit:
Got OCD about the stupid way that the command line handles crappy quoting and wrote the below:
import re
tokens = list()
reading = False
qc = 0
lq = 0
begin = 0
for z in range(len(trial)):
char = trial[z]
if re.match(r'[^\s]', char):
if not reading:
reading = True
begin = z
if re.match(r'"', char):
begin = z
qc = 1
else:
begin = z - 1
qc = 0
lc = begin
else:
if re.match(r'"', char):
qc = qc + 1
lq = z
elif reading and qc % 2 == 0:
reading = False
if lq == z - 1:
tokens.append(trial[begin + 1: z - 1])
else:
tokens.append(trial[begin + 1: z])
if reading:
tokens.append(trial[begin + 1: len(trial) ])
tokens = [re.sub(r'"{1,2}',lambda y:'' if y.group(0) == '"' else '"', z) for z in tokens]
I know this got answered a million year ago, but this works too:
input = '"Y:\DATA\00001\SERVER\DATA.TXT" "V:\DATA2\00002\SERVER2\DATA2.TXT"'
input = input.replace('" "','"').split('"')[1:-1]
Should output it as a list containing:
['Y:\\DATA\x0001\\SERVER\\DATA.TXT', 'V:\\DATA2\x0002\\SERVER2\\DATA2.TXT']
My question Python - Error Caused by Space in argv Arument was marked as a duplicate of this one. We have a number of Python books doing back to Python 2.3. The oldest referred to using a list for argv, but with no example, so I changed things to:-
repoCmd = ['Purchaser.py', 'task', repoTask, LastDataPath]
SWCore.main(repoCmd)
and in SWCore to:-
sys.argv = args
The shlex module worked but I prefer this.