ncov | Nextstrain build for novel coronavirus SARS-CoV-2 | Dataset library
kandi X-RAY | ncov Summary
kandi X-RAY | ncov Summary
This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads. We maintain a number of publicly-available builds, visible at nextstrain.org/ncov.
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Top functions reviewed by kandi - BETA
- R Check additional information
- Adjusts the given string to be used in place
- Add line to simple file
- Checks if a specific location matches a specific location
- Read metadata from a given date
- Search for similar names
- Cleans up string
- Check for recency counts for recency
- Read lab file
- Check for duplicate specifiers
- Read a local configuration file
- Extract special annotations from the metadata file
- Stream the contents of a tar file
- Adjust the coloring for epiweeks
- Generate Tweet Tweet
- Fetch a key from the cache
- Extracts the contents of a tar archive
- Calculate SNPs from a FASTA file
- Reads and returns a dictionary of strain ids
- Fetch a value from the cache
- Prepare a Tweet
- Collects a list of tuples from the input data
- Check if the data is in the CLADE
- Given a metadata file and a metadata column return a list of database identifiers
- Filters the metadata for duplicate strains
- Read data from uk
- Build an ordering file
ncov Key Features
ncov Examples and Code Snippets
Lines of Code : 39License : Permissive (MIT)
Copy# 导入模块
from litncov.user import litUesr
# 新建实例
testme = litUesr("username", "password")
# 判断是否登陆成功
if testme.is_logged():
# 打印用户信息
print(testme.info)
# 打印上次上报信息
print(testme.get_last_record())
# 查询 2021-01-04 至今的上报信息
print( 
License : No LicenseCopystring DIR_WORK = "" # e.g. "/home/git_project"
string DATA_URL = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv" # Data source
string INITIAL_DATE {
"database": {
"default": {
"host": "127.0.0.1",
"port": "3306",
"user": "数据库用户名",
"pwd": "用户密码",
"name": "数据库名",
"max_idle_con": 50,
"max_open_con": 150,
"driver": "mysql"
}
},
"prefix": Community Discussions
Trending Discussions on ncov
QUESTION
In the cmprsk package one of the tests to call crr shows the following:
crr(ftime,fstatus,cov,cbind(cov[,1],cov[,1]),function(Uft) cbind(Uft,Uft^2))
It's the final inline function function(Uft) cbind(Uft,Uft^2) which I am interested in generalizing. This example call to crr above has cov1 as cov and cov2 as cbind(cov[,1],cov[,1]), essentially hardcoding the number of covariates. Hence the hardcoding of the function function(Uft) cbind(Uft,Uft^2) is sufficient.
I am working on some benchmarking code where I would like the number of covariates to be variable. So I generate a matrix cov2 which is has nobs rows and ncovs columns (rather than ncovs being pre-defined as 2 above).
My question is - how do I modify the inline function function(Uft) cbind(Uft,Uft^2) to take in a single column vector of length nobs and return a matrix of size nobs x ncovs where each column is simply the input vector raised to the column index?
Minimal reproducible example below. My call to z2 <- crr(...) is incorrect:
ANSWER
Answered 2022-Feb-13 at 18:12vec <- 1:4
ncovs <- 5
matrix(unlist(Reduce("*", rep(list(vec), ncovs), accumulate= TRUE)), ncol = ncovs)
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 learning rvest.
I intend to scrape my search results. Here is the webpage,
I looked up html_nodes(). There is no what I have seen on the webpage.
What could I do?
Here is the 'body'.
...ANSWER
Answered 2021-Dec-14 at 05:19We can get the title of search results by
QUESTION
I'm making a project that takes google searches via the googlesearch module, and sorts them by the top-level domain. I'll use COVID-19 as an example.
Input:
...ANSWER
Answered 2021-Nov-15 at 01:07One approach would be to create a dictionary of domain extensions along with ranks for sorting the URLs. Then, call sorted with a lambda expression which extracts the domain extension from each URL and does a look up for the sorting value.
QUESTION
how Animated Bar Chart Race Python : How to make a bar change its position automatically. For example, in the below code example while for countries like USA having more values, the bar should gradually move up.
...ANSWER
Answered 2021-Oct-05 at 12:03As far as I know, bar chart tracing using potly is not feasible. There is already a dedicated library that I will use to answer your question. Since the data is at the daily level, it will take a long time to play back, so I will need to resample or summarize the data into years.
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
Suppose I have the below text:
...ANSWER
Answered 2021-May-27 at 22:54The solution was the following:
QUESTION
I have data being sent to me where I need to seek out and identify the ending index of the URL within the string. The one piece of information I have is that the URL will always start with "http". Using this information I can get the starting index. In the case of the example below, that is 13.
...ANSWER
Answered 2021-Apr-01 at 23:44try last index of " "(a space) , make sure it bigger than the urlStart
or the index of first space after urlStart
QUESTION
My code tries to get only the article text from each URLs, however it fails to get every p in the article for every URL. What makes it fails to crawl them?
...ANSWER
Answered 2020-Aug-07 at 07:08It doesn't find all of them because youi haven't requested him to do so.
find will only return the first occurence. If you want to scrape all the
tags in the
findAll method.
QUESTION
tag using python and beautifulsoup
Currently, I'm trying to scrape web content using Python, BeautifulSoup.
after 1st block of code execution, got the below result -
...ANSWER
Answered 2020-Aug-02 at 20:02Looks like you just need the last element inside every "p" tag. Try this:
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