kmers | Counts short k-mers in DNA fragments
kandi X-RAY | kmers Summary
kandi X-RAY | kmers Summary
Counts short k-mers in DNA fragments and do it reasonably fast.
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- Compute kmers lookup .
- Calculate the number of points from a set of points .
- Compute the distance between two kers .
- Initialize k .
- Wrapper for query .
kmers Key Features
kmers Examples and Code Snippets
Community Discussions
Trending Discussions on kmers
QUESTION
I work with single sequence read classification and want to filter based on the quality of classification. However, the output format needs to be changed in order to do this. I have a classification statistics (a score) like below for each read, which represents ["taxonomy":"kmers assigned to that taxonomy" "taxonomy":"kmers assigned to that taxonomy" etc.], and each taxonomy can occur multiple times.
...ANSWER
Answered 2022-Mar-10 at 09:13library(tidyverse)
classification_stats <- c(
"3:1 7:4 0:34 3:7 0:27",
"0:110 561:19 0:37",
"0:3 562:5 0:7 543:55 0:47"
)
read_ID <- c("read1", "read2", "read3")
df <- tibble(read_ID, classification_stats)
df %>%
separate_rows(classification_stats, sep = " ") %>%
separate(classification_stats, into = c("tax", "kmer")) %>%
type_convert() %>%
arrange(-kmer) %>%
nest(tax) %>%
mutate(id = row_number()) %>%
unnest(data) %>%
pivot_wider(names_from = id, values_from = c(kmer, tax))
#> Warning: All elements of `...` must be named.
#> Did you want `data = tax`?
#>
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#> read_ID = col_character(),
#> tax = col_double(),
#> kmer = col_double()
#> )
#> # A tibble: 3 × 27
#> read_ID kmer_1 kmer_2 kmer_3 kmer_4 kmer_5 kmer_6 kmer_7 kmer_8 kmer_9 kmer_10
#>
#> 1 read2 110 NA NA 37 NA NA 19 NA NA NA
#> 2 read3 NA 55 47 NA NA NA NA NA 7 5
#> 3 read1 NA NA NA NA 34 27 NA 7 NA NA
#> # … with 16 more variables: kmer_11 , kmer_12 , kmer_13 ,
#> # tax_1 , tax_2 , tax_3 , tax_4 , tax_5 ,
#> # tax_6 , tax_7 , tax_8 , tax_9 , tax_10 ,
#> # tax_11 , tax_12 , tax_13
QUESTION
I understand the reason why this error is being raised, but not sure how I should go about fixing it. Ideally I would want to avoid using Copy.
ANSWER
Answered 2022-Feb-01 at 08:45If you want to avoid copying/cloning, you need to return a reference. For example:
QUESTION
I'm trying to create an iterator on a library that allows reading a specific file format.
From the docs, to read the file content you need do something like this:
...ANSWER
Answered 2021-Dec-04 at 19:14You'll have to think about 2 major things before:
- Ownership. Currently, you have to make sure your
FileWrappersurvives at least as long as anyIteratorreturned from it by calling itsbegin()(since yourIterators store pointers to data owned by theFileWrapperobject). If you cannot guarantee that, maybe think about usingunique_ptrs orshared_ptrs - Iterator Category. As discussed in the comments, it appears that your database requires you to use "input iterators". They can only be incremented by one (do not provide
operator+(int)) and dereferenced. Indeed, what would the iteratorbegin() + 10look like? If this should advance your file-pointer, then you cannot define the end asbegin() + size()as that would just skip through the file. - Representation. What should an end-iterator look like? A simple choice might be to indicate the end with
database == nullptr. In this case, anoperator!=might look like this:
QUESTION
I have several data frame with format like below. I want to join/merge the data frames by species and extracting kmers from all data frames such that the out contains one column with species and multiple column with kmers, one form each of the files. The kmers column will then be give the name of the file from which it originated.
df1
ANSWER
Answered 2021-Oct-22 at 19:58I'll assume that you've read in the files into a list of frames, named by the basename of the file (with the extension removed). Naming the list-of-frames as dfs, we have
QUESTION
I have a list of sequences:
...ANSWER
Answered 2021-Aug-04 at 23:08Can you elaborate a bit more on what you mean by "frequency for each of the dinucleotide positions"? The following code doesn't compute any kind of percentage or frequency, but it may be helpful for iterating over the columns:
QUESTION
I am parsing a multi-fasta file into single fasta file and I want to create wildcards for each file because the next rule needs to be parallelized for each file. My problem is that I am not able to create a wildcard from the resulting fasta file because the output changes dynamicaly depending on the multi-fasta file I have. Here is my code:
...ANSWER
Answered 2021-Jun-02 at 14:29I think this is what you want...
Input file fasta.fasta is:
QUESTION
I have a list of pandas data frames that I got applying the groupby function and I want to add to them a new column with the frequency of each kmer. I did that with a loop but I got a message warning that I need to use df.loc[index, col_names]. Here it is a link to one example of the csv file: https://drive.google.com/file/d/17vYbIEza7l-1mFnavGGO1QjCjPdhxG7C/view?usp=sharing
...ANSWER
Answered 2021-Apr-05 at 12:28It's an error related SettingWithCopyWarning. It's important — read up on it here. Usually you can avoid it with .loc and by avoiding repeat-slicing, but in some cases where you have to slice repeatedly you can get around it by ending .copy() to the end of the expression. You can learn when and why this is important via the link. For a more precise answer for how this is emerging from you'll code, you'll need to show us an MRCE of your code.
QUESTION
I have stuck with this script it would be great if you could help me with your inputs. My problem is that I think the script is not that efficient - it takes a lot of time to end running.
I have a fasta file with around 9000 sequence lines (example below) and What my script does is:
- reads the first line (ignores lines start with
>) and makes 6mers (6 character blocks) - adds these 6mers to a list
- makes reverse-complement of previous 6mers (list2)
- saves the line if non of the reverse-complement 6mers are in the line.
- Then goes to the next line in the file, and check if it contains any of the reverse-complement 6mers (in list2). If it does, it discards it. If it does not, it saves that line, and reads all reverse complement 6-mers of the new one into the list2 - in addition to the reverse-complement 6-mers that were already there.
my file:
...ANSWER
Answered 2021-Mar-19 at 23:24When I am not mistaken, you can pull the .complement() call outside the inner for for loop. This also gets rid of the first list.
QUESTION
I have a dataframe my_data which looks like this:
...ANSWER
Answered 2021-Feb-28 at 05:24Var1 column is probably character/factor. Convert it to number and then use order to sort.
QUESTION
I have made a recursive program to find set of all possible strings made of certain characters. Here set of characters are - A,C,G,T,-. I am not able to find the reason for the memory error and want to improve the logic.
...ANSWER
Answered 2021-Feb-23 at 04:39You are trying to find all length 20 strings made out of 5 letters. There are 5^20 = 95367431640625 of them. To represent 95 trillion things, each of which takes 20 bytes, would take petabytes of memory. You probably are running this on a computer with gigabytes of memory.
That. Won't. Work.
I can tell you how to make something like this work, but it sounds like an X-Y problem. What were you hoping to do with all of this data, and can you find a way to get by with something more efficient?
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Install kmers
You can use kmers like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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