dna | Human-Readable Data Format

I have a function that accepts an array as the parameters, the function should console.log the array elements into a single array. But what I have is that the array element is printed into separate arrays. My code below

I would like to convert NCBI's Biosample Metadata XML file to CSV, or RDF/XML as a second choice. To do that, I believe I have to learn more about the structure of this file. I can run basic XQueries in BaseX*, like just listing all values, but then I've been using shell tools like sort|uniq -c to count them. I have heard about XSLT transformations and GRDDL in passing, but I don't think a style sheet is provided for this XML document, and I don't know how to create or discover one.

For example, can I get a count of the number of s for each ? Are there any with more than one primary ? What are the most common db attributes of the primary Ids?

Here's a query that shows my maximum level of XQuery sophistication at this point:

I am interested in creating a form of RandomWalk, using DNA sequence to create the walk (eg T = up, A = down etc). I have created the code, however i am wanting to know if it is possible for each of the 4 base letters to be assigned a colour instead of the final plot graph only being in one colour?

I'm trying to make a code for finding siRNAs. For now I've made a code that's just finding all possible siRNAs combinations. I also need to find the best ones, which must contain from 30% to 50% of the GC or CG nucleotides.

This program is searching for the 21 nucleotides length sequences with content of CG or GC from 30 to 50%. For now, my program just generates in one string all of the possible siRNAs with length of 21, but I need to separate the ones with needed amount of GC or CG.

Example of how my program works with K = 2, which means a length of the iRNA sequences from mRNA:

1. inputting the DNA: ATGC
2. It's converting to the mRNA by replacing T with U, so we get: AUGC
3. Making a complementary chain by the Chargaff's rule, A to U, U to A, g to C, C to G, and we get: UACG
4. Now we have a big iRNA, and now we splitting it in all possible ways for get a siRNAs, so: All iRNA combinations ['UA', 'AC', 'CG']

And at the end I want to chose from them the ones that's content C+G nucleotides in range of 30-50%.

Well, there we have only CG with 100, but lets change K to 4, and lets use a ATGCCGTA for the input.

ATCGCGTA All iRNA combinations ['UAGC', 'AGCG', 'GCGC', 'CGCA', 'GCAU']

So, here, the right ones are - UAGC and GCAU

There is an async iterable

I have this code to split a DNA strand into groups of 3. Everything in the result is intended except for that last "None"

I get an error when I want to remove elements from my list.

I want to remove elements in the list ORF300 which are also in list ORF500.

So, I want to keep only elements in the first list which are not in the second one.

Both lists contain lot of DNA sequences. For example ORF300 contains: ["ATTCG","GCTATCT","CGGTATTA"] and ORF500 contains ["GCGGGCATTCGTTG","ATTTTTTTTGCTG","GGGCGGTATTATCGTG"]

So, here I want to remove ATTCG and CGGTATTA from ORF300 and keep GCTATCT because it is not in the ORF500 list but when I start my script:

I have the following table, which i would like to modify:

I want to add rows that contain the following modifications:

1. type: if the value "type" is identical between two rows (it always is in my case), add it again in a separate row of the column "type".

2. position: change the value from intergenic/intragenic to "genome" if (1)

3. ratio: ratio value would be the weighted mean calculated from the ratio of intergenic and intragenic rows of the same type value:
   ((number_intragenic * ratio_intragenic) + (number_intergenic * ratio_intergenic))/(number_intragenic + number_intergenic)

4. number: sum of number values for the same type: sum(number_intergenic + number_intragenic)

5. sum of the percentage values for the same type: sum(percentage_intergenic + percentage_intragenic)

My problem is that I do not know how to add rows to dataframe by making specific calculation from already existing rows. It is easy to add columns using mutate in dplyr. How can I do this for rows?

I would much prefer if the solution is provided in dplyr.

Edit: The formula of the weighted mean was wrong. I had added a + sign instead of a * sign in the following part of the formula: (number_intergenic + ratio_intergenic). It has now been fixed.

I want to read a file, 4 lines by 4 (it's a fastq file, with DNA sequences).
When I read the file one line by one or two by two, there's no issues, but when I read 3 or 4 lines at once, my code crashes (kernel appeared to have died on jupyter notebook). (Uncommenting the last part, or any 3 out of the 4 getline().
I tried with a double array of char (char**) to store the lines, with the same issue.

Any idea what can be the cause ?

Using Python 3.7.3, Cython 0.29, all other libraries updated. File being read is about 1.3GB, machine has 8GB, ubuntu 16.04. Code adapted from https://gist.github.com/pydemo/0b85bd5d1c017f6873422e02aeb9618a