genome | Archived

I'm in a bind please. do you know if i can duplicate the last folder in the path please and add "_genomic.fna.gz" to it for example how to change from this

I have a dataset containing genes identified in different reference genomes. So, the reference genomes are in the Rows and the genes are in the columns of the table. The table is coded as a binary where 0 means the gene is absent and 1 means the gene is present. I made gene accumulation curves, which indicates that the number of genes per genomes is approaching a plateau. Now, I am trying to plot the rarefaction curves using the R-package vegan. I used the following codes:

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 trying to change the separator just between columns 1 and 9. After that, I would like to maintain the original separator.

Those are first lines of my file both when directly reading it and when od -c file is executed:

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 am working on a variant calling Format(.vcf) file. I am separating genotype Allele from individual genome data and calculating the chance of having the specific disease. Based on my analysis I need to implement a condition like : I have two different panda data frame which are extracted from .vcf file

1. Diseases

2.IndividualSNPs

my condition will be like: if number 1.dataframe (Diseases) column 'SNP' is match with number 2. dataframe (individualSNPs) column 'SNP'. then I will check from individualSNPs dataframe cola and colb column.

Table1:(there are hundreds of IDs)

I have a table, one one line per hpo_term so a single patient can have many lines per ID.

I am trying to parse the following data into pandas from a text file: