METABOLIC | scalable high-throughput metabolic | Genomics library

 by   AnantharamanLab Perl Version: v4.0 License: No License

kandi X-RAY | METABOLIC Summary

kandi X-RAY | METABOLIC Summary

METABOLIC is a Perl library typically used in Artificial Intelligence, Genomics applications. METABOLIC has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

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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            kandi-support Support

              METABOLIC has a low active ecosystem.
              It has 126 star(s) with 40 fork(s). There are 7 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 69 open issues and 65 have been closed. On average issues are closed in 69 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of METABOLIC is v4.0

            kandi-Quality Quality

              METABOLIC has 0 bugs and 0 code smells.

            kandi-Security Security

              METABOLIC has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              METABOLIC code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              METABOLIC does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              METABOLIC releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            METABOLIC Key Features

            No Key Features are available at this moment for METABOLIC.

            METABOLIC Examples and Code Snippets

            No Code Snippets are available at this moment for METABOLIC.

            Community Discussions

            QUESTION

            How to extract specific paragraph in a text file and save it in csv file using python?
            Asked 2022-Apr-15 at 14:51

            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 14:51

            You 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:

            Source https://stackoverflow.com/questions/71885186

            QUESTION

            How to export the world of NetLogo 6.2 coloring only the patches that were born turtles?
            Asked 2022-Feb-08 at 03:53

            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 03:53

            I 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).

            Source https://stackoverflow.com/questions/71027107

            QUESTION

            Manipulating dataframe columns
            Asked 2022-Feb-03 at 16:31

            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 16:31

            You can achieve it via pandas explode and apply methods.

            Let's create a sample dataframe first.

            Source https://stackoverflow.com/questions/70974113

            QUESTION

            How to automatically update data when parameters are altered in Android Studio
            Asked 2022-Jan-17 at 13:36

            Basically, I made a fragment with a few EditTexts 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 13:36

            You can use TextWatcher for your EditTexts. When user change text in editText then calculate again

            Source https://stackoverflow.com/questions/70740331

            QUESTION

            Add multiple filtering keywords to a single blog in a gallery?
            Asked 2022-Jan-03 at 16:39

            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 18:43

            Here's what you can change, on line 198:

            Source https://stackoverflow.com/questions/70558659

            QUESTION

            In PostgreSQL, conditionally count rows
            Asked 2021-Sep-27 at 02:09

            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 23:37

            This would appear to be just a simple aggregation,

            Source https://stackoverflow.com/questions/69339709

            QUESTION

            How to get this ggplot legend to be same order as bars?
            Asked 2021-Aug-06 at 14:44

            The data and code I am trying to use:

            ...

            ANSWER

            Answered 2021-Aug-06 at 14:41

            OP here, figured it out:

            Source https://stackoverflow.com/questions/68683070

            QUESTION

            Extracting number after a specific phrase
            Asked 2021-Jun-30 at 00:26

            I've been trying to write two regular expressions to doing the following two tasks:

            1. Pull the numbers after the phrase "EDG ICD HCUP CCS"
            2. 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 18:17

            We 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

            Source https://stackoverflow.com/questions/68024208

            QUESTION

            Mirror two PheWAS plots with ggplot2
            Asked 2021-Jun-13 at 12:48

            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 12:48

            Flipping the 2nd plot

            To achieve this, we need to add two functions:

            • scale_y_reverse: This will flip the y 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

            Source https://stackoverflow.com/questions/67940662

            QUESTION

            R data visualization with ggplot2 - adding colors to 20 variables with RColorBrewer
            Asked 2021-May-28 at 13:55

            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 13:55

            Assuming 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:

            Source https://stackoverflow.com/questions/67739682

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

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            You can download it from GitHub.

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