exome | 🔅 State manager for deeply nested states | State Container library

by Marcisbee TypeScript Version: 2.4.3 License: MIT

X-Ray Key Features Code Snippets Community Discussions(9)Vulnerabilities Install Support

kandi X-RAY | exome Summary

exome is a TypeScript library typically used in User Interface, State Container, React applications. exome has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

As a feature I should also mention, that Exome supports IE as of v0.8.5 even tho it uses Proxy under the hood.

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Support

exome has a low active ecosystem.

It has 120 star(s) with 4 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 4 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of exome is 2.4.3

Quality

exome has no bugs reported.

Security

exome has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

exome is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

exome releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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exome Key Features

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exome Examples and Code Snippets

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Community Discussions

Trending Discussions on exome

Run Snakemake rule one sample at a time

bash loop writing over next file

How to convert XML NER data from the CRAFT corpus to spaCy's JSON format?

How to display all results of my MongoDB query --eval in bash shell without changing in parameters?

MongoDB: How do you find and count in the same query with a specific format?

JQuery Validate "extensions" rule not working

Read complex html file into R with rvest

Converting comma separated file to nested objects json in jq

Snakemake: rule generate strange results

QUESTION

Run Snakemake rule one sample at a time

Asked 2020-Sep-04 at 08:00

I'm creating a Snakemake workflow that will wrap up some of the tools in the nvidia clara parabricks pipelines. Because these tools run on GPU's, they typically can only handle one sample at a time, otherwise the GPU will run out of memory. However, Snakemake shoves all the samples through to Parabricks at one time - seemingly unaware of the GPU memory limits. One solution would be to tell Snakemake to process one sample at a time, thus the question:

How do I get Snakemake to process one sample at a time?

Because parabricks is a licensed product (and therefore not necessarily reproducible), I will show an example of the parabricks rule I am trying to run (pbrun fastq2bam), as well as a minimal reproducible example using open source software (fastqc) which we can work on/from

My parabricks rule - pbrun fastq2bam

Snakefile:

...

ANSWER

Answered 2020-Sep-04 at 07:24

You could try adding threads: 32 to your rule, so snakemake will use all given cores on one rule iteration/sample.

Memory can also be restricted using sth. like

Source https://stackoverflow.com/questions/63733419

QUESTION

bash loop writing over next file

Asked 2019-Dec-23 at 14:52

I am trying to process multiple bam files in a loop using the standard and having an issue where each file overwrites the other. The --bam xxx \ is the only line that will change and the xxx depends on the bam files in the directory. In this example there are three, but that is not always the case. Thank you :).

files in directory --- won't always be three ---

...

ANSWER

Answered 2019-Dec-23 at 14:52

Doesn't look to me like you need the loop at all.

Source https://stackoverflow.com/questions/59457126

QUESTION

How to convert XML NER data from the CRAFT corpus to spaCy's JSON format?

Asked 2019-Dec-17 at 07:00

How to build a named entity recognition(NER) model using spaCy for biomedical NER on CRAFT corpus?

It is difficult for me to pre-process the xml files given in that corpus to any format used by spacy, any little help would be highly appreciated. I first converted the xml files to json format but that was not accepted by spacy. What format of training data does spacy expect? I even tried to build my own NER model but was not able to pre-process the xml files as given in this article.

Here is an example of training an NER model using spacy, including the expected format of training data (from spacy's docs):

...

ANSWER

Answered 2019-Dec-17 at 06:57

Here is some code to get you going. It is not a complete solution, but the problem you posed is very hard, and you didn't have any starter code.

It does not track the identifier or NCBI Homologene properties, but I think those can be stored in a dictionary separately.

Source https://stackoverflow.com/questions/59261444

QUESTION

How to display all results of my MongoDB query --eval in bash shell without changing in parameters?

Asked 2019-Aug-28 at 09:10

When I execute my --eval MongoDB query in bash shell, it returns the 20 first results and then says Type "it" for more. However, I would like to display all of the results.

This question here explains how to query through bash terminal. In the comment section of the accepted answer, someone asks how to display more of the results. Another question asks how to print out more than 20 documents but this changes the default options of MongoDB, something I don't wish to do.

This is the following shell command:

...

ANSWER

Answered 2019-Aug-28 at 09:10

To print all the records, we can use toArray() method. It converts the iterator(returned by find() method) to an array.

The following query can get us the expected output:

Source https://stackoverflow.com/questions/57688438

QUESTION

MongoDB: How do you find and count in the same query with a specific format?

Asked 2019-Apr-03 at 23:12

Using MongoDB, I would like to execute a find and count in a single query and print the result. I previously found this thread but it doesn't answer my question. When I replaced with the adequate information, my query still failed because of memory limit. That's what my documents looks like:

...

ANSWER

Answered 2019-Apr-03 at 23:12

You need $match to apply your filtering condition before you count / return matching documents. Then you can take advantage of $facet which allows you to run multiple aggregations on that filtered data set:

Source https://stackoverflow.com/questions/55501115

QUESTION

JQuery Validate "extensions" rule not working

Asked 2018-Sep-12 at 22:36

I'm using JQuery to validate an HTML form, but the "extension" rule is not working (even though I've included the additional-methods.js file. I've tested my other "rules" (that also come from that js file), and those seem to work fine, so I'm not sure why the extension one isn't.

Here is the html/JS code:

...

ANSWER

Answered 2018-Sep-12 at 22:34

I can see that in line 2 of your code, you have an opened

And all your problems will be fixed.

Source https://stackoverflow.com/questions/52304265

QUESTION

Read complex html file into R with rvest

Asked 2018-Sep-12 at 15:12

I am new to R and stackoverflow so please be gentle, I will try to keep this post as correct as possible. I am working on a project to compare whole exome sequencing (WES) results to proteome data. Our WES facility gives out the data as an html file only, so that I need to read it into R to continue my work.

I tried to follow the DataCamp tutorial for rvest but I think the problem might be that the html files are too complex as what I get is a mess of \t\t\tn\n\t's with some text in between. I suppose the problem is an incorrect html_node?

Here is my R code, followed by a shortened and variant modified HTML.

What I would like to get is a data frame with the same columns as in the html. As in the example, some variants affect multiple transcripts, in these cases single rows/transcript would be perfect but its not a must by any means.

Thank you very much for your help!

Sebastian

...

ANSWER

Answered 2018-Sep-12 at 15:12

Here's the best I can offer you. Note that the output includes the "tooltip text" that pops up when you hover over the data in the Gene column.

Source https://stackoverflow.com/questions/52297953

QUESTION

Converting comma separated file to nested objects json in jq

Asked 2017-Oct-31 at 16:34

I have a CSV file which I would like to parse and obtain a Nested JSON using jq. I have started to use JQ recently and I really like the tool. I understand basic functionalities, but parsing a csv file seems a little difficult especially to print nested objects.

Sample Input

Gene, Exon,Total,Exon Bases, Total Bases, Fraction of Exon bases PIK3CA,PIK3CA_Exon10;chr1;1000;1500,PIK3CA_Exon13;chr1;1000;1500,PIK3CA_Exon14;chr1;1000;1500,1927879,12993042,0.15 NRAS,NRAS_Exon4;chr1;1000;1500,NRAS_Amp_369;chr1;1000;1500,NRAS_Amp_371;chr1;1000;1500,NRAS_Amp_374;chr1;1000;1500,NRAS_Amp_379;chr1;1000;1500,884111,8062107,0.11

Header and Input data explanation

The first column will have one value always. The second column can have multiple exons (1 or more). You can see that it has 3 values in 2nd row and 5 in 3rd row. Exon bases will be the second last column always, Total bases will be last but one and Fraction of exon bases will be the last column.

Note

I have added the header for explanation purposes, it can be removed or modified for processing

Expected output ...

ANSWER

Answered 2017-Oct-08 at 20:43

Here is a solution that (a) assumes there is no header row, in accordance with the comment about the headers (but see below); (b) does not "slurp" the file (i.e., does not read the entire file into memory); and (c) assumes a version of jq with inputs. (If your jq does not have inputs, it would be very easy to modify the following accordingly.)

Source https://stackoverflow.com/questions/46632107

QUESTION

Snakemake: rule generate strange results

Asked 2017-Sep-21 at 09:17

I create this rule:

...

ANSWER

Answered 2017-Sep-21 at 09:17

Since it works perfectly with the second way to write the output, I would suggest to use this one. What's happening is the following:

since in your rule picard the input is:
"mapped_reads/merged_samples/{sample}.dedup.bam"
you must have a rule that creates this file as output. and in your rule picard the output is: "mapped_reads/merged_samples/{sample}_rg.dedup.bam"

So when you ask in your expand:
"mapped_reads/merged_samples/{sample}_rg.dedup.bam"
snakemake does not know if it has to use your rule picard with sample as the wildcard or your other rule with sample_rg as the wildcard since they both end and begin with the same pattern.

To resume: try not to use two outputs with a wildcard that can be expanded. Here both you outputs:
"mapped_reads/merged_samples/{sample}.dedup.bam"
"mapped_reads/merged_samples/{sample}_rg.dedup.bam"
begin and end with exactly the same pattern.

When you use: "mapped_reads/merged_samples/{sample}.dedup_rg.bam"
as output, the wildcard cannot be expanded!

Source https://stackoverflow.com/questions/46301028

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

Vulnerabilities

No vulnerabilities reported

Install exome

To install the stable version:. This assumes you are using npm as your package manager.

Support

This package works with IE. Even tho it uses Proxy, we can get by not using it on IE, but no performance penalty in other browsers that would utilize Proxy. To run Exome on IE, you must have Symbol and Promise polyfills and down-transpile to ES5 as usual. And that's it! Do not use Proxy polyfill! Most Proxy polyfills will just break Exome because of huge limitations in them.

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