SARS-CoV-2 | Ongoing analysis of COVID-19 using Galaxy

 by   galaxyproject Jupyter Notebook Version: 0.5 License: MIT

kandi X-RAY | SARS-CoV-2 Summary

kandi X-RAY | SARS-CoV-2 Summary

SARS-CoV-2 is a Jupyter Notebook library. SARS-CoV-2 has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures

            kandi-support Support

              SARS-CoV-2 has a low active ecosystem.
              It has 125 star(s) with 80 fork(s). There are 32 watchers for this library.
              It had no major release in the last 12 months.
              There are 9 open issues and 22 have been closed. On average issues are closed in 6 days. There are 7 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of SARS-CoV-2 is 0.5

            kandi-Quality Quality

              SARS-CoV-2 has no bugs reported.

            kandi-Security Security

              SARS-CoV-2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              SARS-CoV-2 is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              SARS-CoV-2 releases are available to install and integrate.

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            SARS-CoV-2 Key Features

            No Key Features are available at this moment for SARS-CoV-2.

            SARS-CoV-2 Examples and Code Snippets

            No Code Snippets are available at this moment for SARS-CoV-2.

            Community Discussions


            Tensorflow Keras text_to_sequence return a list of lists
            Asked 2022-Jan-12 at 09:44

            i have a problem in text_to_sequence in tf.keras



            Answered 2022-Jan-12 at 09:43

            You should not use text_to_word_sequence if you are already using the class Tokenizer. Since the tokenizer repeats what text_to_word_sequence actually does, namely tokenize. Try something like this:



            How to remove element tags from results, Web Scraping Articles with Python
            Asked 2022-Jan-12 at 05:45

            I've recently been teaching myself python and instead of diving right into courses I decided to think of some script ideas I could research and work through myself. The first I decided to make after seeing something similar referenced in a video was a web scraper to grab articles from sites, such as the New York Times. (I'd like to preface the post by stating that I understand some sites might have varying TOS regarding this and I want to make it clear I'm only doing this to learn the aspects of code and do not have any other motive -- I also have an account to NYT and have not done this on websites where I do not possess an account)

            I've gained a bit of an understanding of the python required to perform this as well as began utilizing some BeautifulSoup commands and some of it works well! I've found the specific elements that refer to parts of the article in F12 inspect and am able to successfully grab just the text from these parts.

            When it comes to the body of the article, however, the elements are set up in such a way that I'm having troubling grabbing all of the text and not bringing some tags along with it.

            Where I'm at so far:



            Answered 2022-Jan-12 at 05:45

            Select the paragraphs more specific, while adding p to your css selector, than item is the paragraph and you can simply call .text or if there is something to strip -> .text.strip() or .get_text(strip=True):



            selecting an element by a tag name and class name
            Asked 2021-Dec-10 at 20:24

            I am trying to capture a tags inside a header with known class name.

            inspect element:



            Answered 2021-Dec-10 at 20:24

            You can't use getElementsByTagName method after getElementsByClassName, you should use:



            Pandas Iterate over dataframe to relate cells via their related content
            Asked 2021-Dec-01 at 21:48

            The title may not be the full description of what I want to do, but I will try to fully explain what I am working with. I have a pandas Dataframe that contains all data from files in a directory.



            Answered 2021-Dec-01 at 21:48

            There are basically two steps here:

            1. Get the cell number so we can match files belonging to the same experiment and cell number.
            2. Use groupby() to perform the matching.

            After that, you can loop over the groupby, and get rows belonging to a single experiment.




            Accessing files in a remotely snakedeploy-ed workflow
            Asked 2021-Oct-01 at 14:08

            When using snakedeploy with a workflow remotely stored on github, what is the current best practice for that remote workflow to access files from its own "workflow/scripts/" or "resources/" directories?

            E.g.: running



            Answered 2021-Oct-01 at 14:08

            As of snakemake version 6.8.1, the documentation got updated, and there is now an officially documented function for fetching such files:

            This function internally does indeed rely on the infer_source / sequence.

            It does return a tupple with:

            • the path
            • the content of the file (from the cached content)
            • automatic type identification
            • whether file is local.



            remove - using regular expression
            Asked 2021-Sep-04 at 19:49
            import regex as re
            def tokenize(text):
                return re.findall(r'[\w-][-]*\p{L}[\w-]*',text)
            text ="let's defeat the SARS-coV-2 delta variant together in 2021!"
            tokens= tokenize(text)


            Answered 2021-Sep-04 at 03:11

            You can simplify your regex pattern by just using re.split() on the characters that you consider as word-separators such as apostrophe ', space , dash -, etc.



            simplexml_load_file not showing all xml attributes
            Asked 2021-Aug-09 at 18:02

            I'm trying to pull xml data from some link with simplexml_load_file.
            This one xml node I am trying to access is an array with 4 elements.
            Each element has a label which I am trying to read.
            I try to read each label using the attributes() function, but for some reason the function only returns the first node label.



            Answered 2021-Aug-09 at 18:02

            SimpleXML::attributes only appears returns the attributes from the first element in the set.

            Although undocumented, this is logical, because the attributes are keyed based on the attribute name, and PHP does not allow reuse of the "Label" key in this way. Even if they weren't, I guess it might be hard to distinguish which attributes applied to which elements.

            You'll need to rewrite as a foreach loop or similar.



            Possible to retain line breaks in pandas read_html when making data frame from html table?
            Asked 2021-Jul-14 at 21:00

            I'm trying to convert a scraped HTML table into a dataframe in python using pandas read_html. The problem is that read_html brings in a column of my data without breaks, which makes the content of those cells hard to parse. In the original HTML, each "word" in the column is separated by a break. Is there a way to keep this formatting or otherwise keep the "words" separated when converting to a data frame?



            Answered 2021-Jul-14 at 21:00


            snakemake - define input for aggregate rule without wildcards
            Asked 2021-Jun-08 at 15:40

            I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex and artic minion.

            The snakemake that I wrote has the following steps:

            1. zip all the fastq files for all barcodes (rule zipFq)
            2. perform read filtering with guppyplex (rule guppyplex)
            3. call the artic minion pipeline (rule minion)
            4. move the stderr and stdout from qsub to a folder under the working directory (rule mvQsubLogs)

            Below is the snakemake that I wrote so far, which works



            Answered 2021-Jun-08 at 15:40

            The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

            Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

            First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

            It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

            Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

            However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

            Edit: Dummy test example:



            How to fix div overlapping while using a customized div in a container-fluid (Bootstrap)
            Asked 2021-Apr-19 at 03:54

            I am new to HTML, CSS and Bootstrap. I got the problem with overlapping divs when resize the screen to be smaller. The problem appeared when I used the container-fluid as a section and I used a customized div to have the header of the section. I tried to change the display property of my customized div (the header of the section) but it did not work. I have no idea where the problem. I hope you guys could hint me an idea to fix this one. Thank you all in advance and sorry if the question is a bit silly.

            This is my HTML:



            Answered 2021-Apr-19 at 03:54

            Your solution is to remove almost every time in CSS that you manually set the height property. I would advise to never do this if you can avoid it, especially for divs that just contain text.

            I wish I could give a more academic answer, but I don't have the experience to do so.

            You can read more here about setting the height property if you still desire to do so


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


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