METABOLIC | scalable high-throughput metabolic | Genomics library
kandi X-RAY | METABOLIC Summary
kandi X-RAY | METABOLIC Summary
METabolic And BiogeOchemistry anaLyses In miCrobes Current Version: 4.0 Tested on: Linux Ubuntu 16.04.6 LTS (GNU/Linux 4.15.0-101-generic x86_64) (June 2020). This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets. These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or pure culture sequenced genomes. METABOLIC has two main implementations, which are METABOLIC-G and METABOLIC-C. METABOLIC-G.pl allows for generation of metabolic profiles and biogeochemical cycling diagrams of input genomes and does not require input of sequencing reads. METABOLIC-C.pl generates the same output as METABOLIC-G.pl, but as it allows for the input of metagenomic read data, it will generate information pertaining to community metabolism. It can also calculate the genome coverage. The information is parsed and diagrams for elemental/biogeochemical cycling pathways (currently Nitrogen, Carbon, Sulfur and "other") are produced.
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QUESTION
I have a text file which contains the information about Title, Author, Abstract, DOI etc. I want to extract only the abstract and store it in a dataframe. I tried using below code, but I'm getting Author information and DOI, I only want the middle paragraph between Author information: and DOI:. How do I get that specific paragraph and store it in a dataframe
...ANSWER
Answered 2022-Apr-15 at 14:51You can try:
- retrieving the whole content of the file as a string
- splitting on 'Author information:\n', to retrieve infos about every single paper
- getting the index 1 of your papers, to retrieve the abstracts
Here's the code:
QUESTION
I don't really know how to export the following output...
I have 16 turtles profiles, which refers to the non-repeating combination of habitatcover types (see ValidHabs variable)
In the model, it starts with 10 turtles that can reproduce or die.
I would like to generate an output in which the whole world turns white and paints magenta only where turtles were born, that is, the 10 turtles that started the world and then the new turtles that emerged through the reproduction process. And that this came out by turtle profile. I have looked up the NetLogo dictionary and I believe I should use the export-view command
But, I still couldn't execute in a simple code that can only export in image form the patches that only existed turtle (painted in magenta) at the end of all ticks (that is, all patches that had turtles taking into account all ticks ) for that turtle profile.
What I've managed to do so far is below.
Any kind of help will be very welcome :)
Thanks in advance!
...ANSWER
Answered 2022-Feb-08 at 03:53I think the best way to track this is a patches-own
variable to track if a turtle was ever born on the patch
. In this example code I've called that turtle-born-here
, set the variable to false
in the setup, then update the variable any time a turtle
is 'born' (either on setup, or during go
).
QUESTION
I have a pandas dataframe that I want to manipulate. Here's an example of the data:
As you can see we have 3 columns. Column proteins
has multiple elements separated with a comma, whereas column term description
only has a single element per row. My aim is to reverse this and have a column with single elements from proteins
and another column with multiple elements from term description
. To explain this by an example if proteins CYP51A1
fall under the term description
metabolic process
and organic substance metabolic process
I want my dataframe to look like this:
ANSWER
Answered 2022-Feb-03 at 16:31You can achieve it via pandas explode and apply methods.
Let's create a sample dataframe first.
QUESTION
Basically, I made a fragment with a few EditText
s where the user can insert data about himself, such as bodyweight, height, age, etc.. I also added a TextView
which displays that person's basal metabolic rate depending on the data that was inserted, but the problem is, whenever I change the person's information, it doesn't automatically update.
I'm assuming this is because the calculations are made inside the onCreateView
method, thus it only calculates BMR if I statically pre-insert the respective data.
So, how can I make it so whenever I change the value of a certain variable (f.e age) it will also automatically re-calculate the value of the person's BMR?
JAVA
...ANSWER
Answered 2022-Jan-17 at 13:36You can use TextWatcher for your EditTexts. When user change text in editText then calculate again
QUESTION
I am planning to add a filtering feature to my website blogs. For this, each blog post will be associated with a keyword. Selecting these keywords will show/filter all the blogs associated with that specific keyword category.
In the code below, I have separated my blogs into 3 categories (Forest, Birds and Sea). However, I also want some of the blogs to be associated with multiple keywords (two or three), see the 'Forest Birds' section in the snippet below. If someone can help me with how to do it, that would be great.
...ANSWER
Answered 2022-Jan-02 at 18:43Here's what you can change, on line 198:
QUESTION
Background
I'm a novice Postgres user running a local server on a Windows 10 machine. I've got a dataset g
that looks like this:
ANSWER
Answered 2021-Sep-26 at 23:37This would appear to be just a simple aggregation,
QUESTION
The data and code I am trying to use:
...ANSWER
Answered 2021-Aug-06 at 14:41OP here, figured it out:
QUESTION
I've been trying to write two regular expressions to doing the following two tasks:
- Pull the numbers after the phrase "EDG ICD HCUP CCS"
- Pull the words after "EDG ICD HCUP CCS 159 (PREDICTIVE MODELS-VERSION 1.0)-"
I'd like to have the numbers stored in a column named "category" and the words stored in "diagnosis"
The strings are located in the column name "GROUPER_NAME".
...ANSWER
Answered 2021-Jun-17 at 18:17We can use sub
from base R
. Capture the digits (\\d+
) after the prefix substring, and the characters after the )
and -
. In the replacement, specify the backreference (\\1
, \\2
) of the captured group, and read them into a two column data.frame with read.csv
QUESTION
I have two PheWAS plots, and the number of categories (x axis, 20 categories) is the same in case of both. I would like to put them on the same plot, mirroring one of them on the y axis, but leaving the x axis titles in the middle.
Example data:
...ANSWER
Answered 2021-Jun-13 at 12:48Flipping the 2nd plot
To achieve this, we need to add two functions:
scale_y_reverse
: This will flip they
axis; 0 is at the top, 10 at the bottom.scale_x_discrete(position = top)
: This will put the x-axis at the top.
Fixing the y-axis limits
It would be best to keep the same y-axis limits for both plots, to make them comparable. As such, we have to supply ylim()
to the first plot. For the second plot, we already have scale_y_reverse
, so we can supply our limits there.
Fixing the x labels
Since you only want the labels to appear once, you'd have to use element_blank()
for theme(axis.text.x)
and theme(axis.title.x)
in the 2nd plot. Similarly, I would remove the x-axis title in the first plot to keep it balanced.
Combining the plots
Now, you want to combine the plots. However, the first plot has a lot of information on the x-axis, while the second plot doesn't. This means they have different heights. I like to use cowplot::plot_grid
for combining plots, because it allows you to set the relative height of the plots. In this case, we can use it to account for the height difference between the two plots.
Final code
QUESTION
I am trying to visualize data with ggplot2, and add 20 different colors to the 20 categories I have in "description". Without the colors, the script works perfectly (only black). However, in any way I want to add color it either stays black, or with the script below I get the following error:
Error: Aesthetics must be either length 1 or the same as the data (2265723): colour
This should not be a problem, as "Pastel1" has 255 colors and I created a lenght variable.
dataset (description has 20 categories):
...ANSWER
Answered 2021-May-28 at 13:55Assuming that you wish to colour by the variable description
, you can use the ColorBrewer palette with colourCount
number of elements by adding scale_colour_manual(values = getPalette(colourCount))
to the ggplot object. And change colour = description
in the aesthetics:
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