Now, I need to find a way in which Python can find the codon position number 5 of the above code and extract that sequence until position 12 (ATGG*CTTTACCTCGTC*TCACAGGAG). So the output should be something like this:
>CCODE1112_5..11
CTTTACCTCGTC
How can I tell python to get the begin value after the first "_" and the end value after ".." so it can do it automatically? ? THANKS!!!
def extractseq( queryseq , begin=5, end =12):
queryseq=queryseq.split('\n')#transform the string in a list of lines included in the string
return queryseq[1][begin-1:end-1]
I think this function should work, beware of the index which begin at 0 in python
after written that in your script you just have to call the function subs=extractseq(seq,5,12)
ok sorry so if you want to extract the 5 and the 12 included in the substring one way to do that easly is:
substring=queryseq.split('\n')[0].split('_')[1].split('...')#extraction of the substring
begin=substring[0]
end = substring[1]
I'd probably (sigh) use a regex to extract 5 and 12 from CCODE1112_5..12_ABC.
Then convert the extracted strings to int's.
Then use the int's as indexes in a string slice on the DNA data.
For the regex:
regex = re.compile(r'^[^]*(\d+)..(\d+)_.*$')
regex.match('CCODE1112_5..12_ABC')
match = regex.match('CCODE1112_5..12_ABC')
match.group(1)
'5'
match.group(2)
'12'
To convert those to int's, use int(match.group(1)), for example.
Then your indices are 1-based, while python's are 0-based. Also, python's starting point for a slice is at the value you want, and python's ending point for a slice is one past the value you want. So subtract one from group(1) and leave group(2) alone.
So something like:
substring = dna_data[left_point-1:right_point]
Related
There is this typical problem: given a list of values, check if they are present in an array.
In awk, the trick val in array does work pretty well. Hence, the typical idea is to store all the data in an array and then keep doing the check. For example, this will print all lines in which the first column value is present in the array:
awk 'BEGIN {<<initialize the array>>} $1 in array_var' file
However, it is initializing the array takes some time because val in array checks if the index val is in array, and what we normally have stored in array is a set of values.
This becomes more relevant when providing values from command line, where those are the elements that we want to include as indexes of an array. For example, in this basic example (based on a recent answer of mine, which triggered my curiosity):
$ cat file
hello 23
bye 45
adieu 99
$ awk -v values="hello adieu" 'BEGIN {split(values,v); for (i in v) names[v[i]]} $1 in names' file
hello 23
adieu 99
split(values,v) slices the variable values into an array v[1]="hello"; v[2]="adieu"
for (i in v) names[v[i]] initializes another array names[] with names["hello"] and names["adieu"] with empty value. This way, we are ready for
$1 in names that checks if the first column is any of the indexes in names[].
As you see, we slice into a temp variable v to later on initialize the final and useful variable names[].
Is there any faster way to initialize the indexes of an array instead of setting one up and then using its values as indexes of the definitive?
No, that is the fastest (due to hash lookup) and most robust (due to string comparison) way to do what you want.
This:
BEGIN{split(values,v); for (i in v) names[v[i]]}
happens once on startup and will take close to no time while this:
$1 in array_var
which happens once for every line of input (and so is the place that needs to have optimal performance) is a hash lookup and so the fastest way to compare a string value to a set of strings.
not an array solution but one trick is to use pattern matching. To eliminate partial matches wrap the search and array values with the delimiter. For your example,
$ awk -v values="hello adieu" 'FS values FS ~ FS $1 FS' file
hello 23
adieu 99
I am trying to create a string array which will be fed with string values read from a text file this way:
labels = textread(file_name, '%s');
Basically, for each string in each line of the text file file_name I want to put this string in 10 positions of a final string array, which will be later saved in another text file.
What I do in my code is, for each string in file_name I put this string in 10 positions of a temporary cell array and then concatenate this array with a final array this way:
final_vector='';
for i=1:size(labels)
temp_vector=cell(1,10);
temp_vector{1:10}=labels{i};
final_vector=horzcat(final_vector,temp_vector);
end
But when I run the code the following error appears:
The right hand side of this assignment has too few values to satisfy the left hand side.
Error in my_example_code (line 16)
temp_vector{1:10}=labels{i};
I am too rookie in cell strings in matlab and I don't really know what is happening. Do you know what is happening or even have a better solution to my problem?
Use deal and put the left hand side in square brackets:
labels{1} = 'Hello World!'
temp_vector = cell(10,1)
[temp_vector{1:10}] = deal(labels{1});
This works because deal can distribute one value to multiple outputs [a,b,c,...]. temp_vector{1:10} alone creates a comma-separated list and putting them into [] creates the output array [temp_vector{1}, temp_vector{2}, ...] which can then be populated by deal.
It is happening because you want to distribute one value to 10 cells - but Matlab is expecting that you like to assign 10 values to 10 cells. So an alternative approach, maybe more logic, but slower, would be:
n = 10;
temp_vector(1:n) = repmat(labels(1),n,1);
I also found another solution
final_vector='';
for i=1:size(labels)
temp_vector=cell(1,10);
temp_vector(:,1:10)=cellstr(labels{i});
final_vector=horzcat(final_vector,temp_vector);
end
I have a matlab cell array of size 20x1 elements. And all the elements are string like 'a12345.567'.
I want to substitute part of the string (start to 9th index) of all the cells.
so that the element in matrix will be like 'a12345.3'.
How can I do that?
You can use cellfun:
M = { 'a12345.567'; 'b12345.567' }; %// you have 20 entries like these
MM = cellfun( #(x) [x(1:7),'3'], M, 'uni', 0 )
Resulting with
ans =
a12345.3
b12345.3
For a more advanced string replacement functionality in Matlab, you might want to explore strrep, and regexprep.
Another method that you can use is regexprep. Use regular expressions and find the positions of those numbers that appear after the . character, and replace them with whatever you wish. In this case:
M = { 'a12345.567'; 'b12345.567' }; %// you have 20 entries like these - Taken from Shai
MM = regexprep(M, '\d+$', '3');
MM =
'a12345.3'
'b12345.3'
Regular expressions is a framework that finds substrings within a larger string that match a particular pattern. In our case, \d is the regular expression for a single digit (0-9). The + character means that we want to find at least one or more digits chained together. Finally the $ character means that this pattern should appear at the end of the string. In other words, we want to find a pattern in each string such that there is a number that appears at the end of the string. regexprep will find these patterns if they exist, and replace them with whatever string you want. In this case, we chose 3 as per your example.
I have some which converts a cell array of strings into a cell array of characters.
Note. For a number of reasons, both the input (C) and the output (C_itemised) must be cell arrays.
The cell array of strings (C) is as follows:
>> C(1:10)
ans =
't1416933446'
''
't1416933446'
''
't1416933446'
''
't1416933446'
''
't1416933446'
''
I have only shown a portion of the array here. In reality it is ~28,000 rows in length.
I have some code which does this, although it is very inefficient. The cellstr function takes up 72% of the code's time, as it is currently called thousands of times. The code is as follows:
C_itemised=cell(length(C),500);
for i=3:length(C)
temp=char(C{i});
for j=1:length(temp)
C(i-2,j)=cellstr(temp(j));
end
end
I have a feeling that some minor modifications could take out the inner loop, thus cutting down the overall running time substantially. I have tried a number of ways to do this, but I think I keep getting confused about whether to use {} or (), and haven't been able to find anything online that can help me. Can anyone see a way to make the code more efficient?
Please also note that this function is used in conjunction with other functions, and does work, although it is running slower than would be ideal. Therefore, I do not wish to change the format of C_itemised.
EDIT:
(A sample of) the output of my current function is:
C_itemised(1,1:12)
ans =
Columns 1 through 12
't' '1' '4' '1' '6' '9' '3' '3' '4' '4' '6' []
One thing I can suggest is to use the undocumented function sprintfc. This function is hidden from normal use in MATLAB, but it is used internally with a variety of other functions. Mainly, if you tried doing help sprintfc, it'll say that there's no function found! It's cool to sniff around the source sometimes!
How sprintfc works is that you provide it a formatting string, much like printf, and the data you want printed. It will take each individual element in the data and place them into individual cell arrays. As an example, supposing I had a string D = 'abcdefg';, if we did:
out = sprintfc('%c', D);
We get:
>> celldisp(out)
out{1} =
a
out{2} =
b
out{3} =
c
out{4} =
d
out{5} =
e
out{6} =
f
out{7} =
g
As such, it takes each element in your string and places them as individual characters serving as individual elements in a new cell array. The %c formatting string means that we want to print a single character per element. Check out the link to Undocumented MATLAB that I posted above if you want to learn more!
Therefore, try simplifying your loop to this:
C_itemised=cell(length(C));
for i=1:length(C)
C_itemised{i} = sprintfc('%c', C{i});
end
C_itemised will be a cell array, where each element C_itemised{i} is another cell array, with each element in this cell array being a single character that is composed of the string C{i}.
Minor Note
You said you were confused about {} and () in MATLAB for cells. {} is used to access individual elements inside the cell. So doing C{1} for example will grab whatever is stored in the first element of the cell array. () is used to slice and index into the cells. For example, if you wanted to make another cell array that is a subset of the current one, you would do something like C(1:3). This will create a three element cell array which is composed of the first three cells in C.
I want to check if any string in an array of strings is a prefix of any other string in the same array. I'm thinking radix sort, then single pass through the array.
Anyone have a better idea?
I think, radix sort can be modified to retrieve prefices on the fly. All we have to do is to sort lines by their first letter, storing their copies with no first letter in each cell. Then if the cell contains empty line, this line corresponds to a prefix. And if the cell contains only one entry, then of course there are no possible lines-prefices in it.
Here, this might be cleaner, than my english:
lines = [
"qwerty",
"qwe",
"asddsa",
"zxcvb",
"zxcvbn",
"zxcvbnm"
]
line_lines = [(line, line) for line in lines]
def find_sub(line_lines):
cells = [ [] for i in range(26)]
for (ine, line) in line_lines:
if ine == "":
print line
else:
index = ord(ine[0]) - ord('a')
cells[index] += [( ine[1:], line )]
for cell in cells:
if len(cell) > 1:
find_sub( cell )
find_sub(line_lines)
If you sort them, you only need to check each string if it is a prefix of the next.
To achieve a time complexity close to O(N2): compute hash values for each string.
Come up with a good hash function that looks something like:
A mapping from [a-z]->[1,26]
A modulo operation(use a large prime) to prevent overflow of integer
So something like "ab" gets computed as "12"=1*27+ 2=29
A point to note:
Be careful what base you compute the hash value on.For example if you take a base less than 27 you can have two strings giving the same hash value, and we don't want that.
Steps:
Compute hash value for each string
Compare hash values of current string with other strings:I'll let you figure out how you would do that comparison.Once two strings match, you are still not sure if it is really a prefix(due to the modulo operation that we did) so do a extra check to see if they are prefixes.
Report answer