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kandi X-RAY | SARS-CoV-2 Summary
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QUESTION
i have a problem in text_to_sequence in tf.keras
...ANSWER
Answered 2022-Jan-12 at 09:43You 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:
QUESTION
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:
...ANSWER
Answered 2022-Jan-12 at 05:45Select 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):
QUESTION
I am trying to capture a tags inside a header with known class name.
inspect element:
...ANSWER
Answered 2021-Dec-10 at 20:24You can't use getElementsByTagName method after getElementsByClassName, you should use:
QUESTION
ANSWER
Answered 2021-Dec-01 at 21:48There are basically two steps here:
- Get the cell number so we can match files belonging to the same experiment and cell number.
- Use groupby() to perform the matching.
After that, you can loop over the groupby, and get rows belonging to a single experiment.
Example:
QUESTION
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
...ANSWER
Answered 2021-Oct-01 at 14:08As of snakemake version 6.8.1, the documentation got updated, and there is now an officially documented function for fetching such files: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#accessing-auxiliary-source-files
This function internally does indeed rely on the infer_source / sourcecache.open 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.
QUESTION
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)
print("|".join(tokens))
ANSWER
Answered 2021-Sep-04 at 03:11You 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.
QUESTION
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.
ANSWER
Answered 2021-Aug-09 at 18:02SimpleXML::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.
QUESTION
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?
ANSWER
Answered 2021-Jul-14 at 21:00Maybe...
QUESTION
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:
- zip all the
fastqfiles for all barcodes (rulezipFq) - perform read filtering with
guppyplex(ruleguppyplex) - call the
artic minionpipeline (ruleminion) - 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
...ANSWER
Answered 2021-Jun-08 at 15:40The 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:
QUESTION
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:
...ANSWER
Answered 2021-Apr-19 at 03:54Your 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
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