picard | Preconditioned ICA for Real Data

by pierreablin Python Version: Current License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | picard Summary

picard is a Python library. picard has no bugs, it has build file available, it has a Permissive License and it has high support. However picard has 1 vulnerabilities. You can download it from GitHub.

Preconditioned ICA for Real Data

Support

Quality

Security

License

Reuse

Support

picard has a highly active ecosystem.

It has 73 star(s) with 10 fork(s). There are 7 watchers for this library.

It had no major release in the last 6 months.

There are 2 open issues and 13 have been closed. On average issues are closed in 26 days. There are 1 open pull requests and 0 closed requests.

It has a negative sentiment in the developer community.

The latest version of picard is current.

Quality

picard has 0 bugs and 0 code smells.

Security

picard has 1 vulnerability issues reported (0 critical, 1 high, 0 medium, 0 low).

picard code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

picard is licensed under the BSD-3-Clause License. This license is Permissive.

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

Reuse

picard releases are not available. You will need to build from source code and install.

Build file is available. You can build the component from source.

picard saves you 389 person hours of effort in developing the same functionality from scratch.

It has 926 lines of code, 43 functions and 14 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed picard and discovered the below as its top functions. This is intended to give you an instant insight into picard implemented functionality, and help decide if they suit your requirements.

Perform a Picard clustering
Computes the gradient of the Fourier transform
Compute the symmetric symmetry operator
Core Picard - Spearman Analysis
Calculate the loss function
Regularize the Hessian
Checks the density of a Gaussian distribution
Checks if the given seed is a numpy RandomState instance
Perform FastICA analysis
Perform a line search
Fit the model to the data
Perform a Picard analysis
Permute matrix A
Fit an ICA using a method
Autolabel the plot
Return a list of subdirectories in the given package root
Calculate the gradient of the covariance matrix

Get all kandi verified functions for this library.

picard Key Features

No Key Features are available at this moment for picard.

picard Examples and Code Snippets

No Code Snippets are available at this moment for picard.

Community Discussions

Trending Discussions on picard

How to extract a number marked with specific word from text string in Google Data Studio

How do I sort a Binary Search Tree from greatest to least?

How do I stop a Binary Search Tree Traversal?

Swift function that can return various types

Mongodb 4.4.x - findOneAndUpdate() with $set and $push

Filter users with a join table

How to include shell script suite in docker file

Docker image generating error for /usr/bin/java

Merge vcf files in snakemake

How to use singularity and conda wrappers in Snakemake

QUESTION

How to extract a number marked with specific word from text string in Google Data Studio

Asked 2021-May-05 at 14:13

I have a text string that contains several instances of numbers, example of the data is below.

I am trying to extract the number of keys (the number that is followed by the text -keys). I tried several REGEXP_EXTRACT patterns without luck.

{38-keys,fit-out,closed,eddy-tamy,datechange-feb2025,staff-onboard,sandy-brighton,open-dec2020}

{same-year,budgeted,signature-done,mark-picard,hotel,5-keys}

{active,building,itsa-signed,2322-keys,pending-signature,next-year-(construction),opening-feb2024}

...

ANSWER

Answered 2021-Apr-01 at 09:27

0) Summary

Use #1 OR #2 OR #3 below (added two additional suggestions as the author received an error with #1 and then #2 in regards to the CAST function which may be a result of spacing, Data Source (PostgreSQL) specific or another issue).

1) With CAST

It can be achieved by using the Calculated Field below (where Field represents the respective field name) which extracts all digits immediately preceding -keys; the CAST function was added to ensure that the field Type is Number (the default field Type of REGEXP_EXTRACT values are Text); also, for future reference, the Raw Input Literal R was used so that \d represents the sequence for a digit vs the default (without R) in Google Data Studio, which requires two back slashes (\\d):

Source https://stackoverflow.com/questions/66899431

QUESTION

How do I sort a Binary Search Tree from greatest to least?

Asked 2021-Apr-04 at 19:24

I need to return an array of nodes sorted from high to low. At the moment I am trying to implement an inorder traversal which gives me the exact opposite of what I'm looking for.

The tree looks like:

...

ANSWER

Answered 2021-Apr-04 at 18:34

You should just swap the two if statements where you make a recursive call, so that you first visit rightReport and then later leftReport.

Source https://stackoverflow.com/questions/66944539

QUESTION

How do I stop a Binary Search Tree Traversal?

Asked 2021-Apr-03 at 07:22

I need to traverse a binary search tree and return an array of the leaf nodes. At the moment I am traversing through the entire tree and returning one node at a time.

My tree looks like:

...

ANSWER

Answered 2021-Apr-03 at 07:22

findOfficersWithNoDirectReports() {
    // If this is a leaf node, return the officer name
    if (!this.leftReport && !this.rightReport) {
      return [this.officerName]
    }

    // Otherwise, combine the left and right results 
    val result = []
    if (this.leftReport) {
      result = result.concat(this.leftReport.findOfficersWithNoDirectReports());
    }
    if (this.rightReport) {
      result = result.concat(this.rightReport.findOfficersWithNoDirectReports());
   }
    return result;

  }

Source https://stackoverflow.com/questions/66925947

QUESTION

Swift function that can return various types

Asked 2021-Mar-06 at 17:35

Is it possible for a function to return a specific Data Type based on the parameter entered?

Here's an example of what I'm trying to do:

I've defined different datatypes that will hold data from an API call

...

ANSWER

Answered 2021-Mar-06 at 17:13

You can use protocols:

Create protocol with given fields, and make all DataType1,2 etc classes conform to it:

Source https://stackoverflow.com/questions/66508294

QUESTION

Mongodb 4.4.x - findOneAndUpdate() with $set and $push

Asked 2021-Feb-26 at 23:16

I am trying to do a findOneAndUpdate() to Find a document and update it in one atomic operation

...

ANSWER

Answered 2021-Feb-26 at 23:16

Try this, probably will work:

Source https://stackoverflow.com/questions/66393919

QUESTION

Filter users with a join table

Asked 2020-Nov-09 at 16:53

I have tables for users, tags, and join table taggings.

I'm currently using scope to filter users through different variables, for example:

...

ANSWER

Answered 2020-Nov-09 at 16:53

You can get a count and use having to stipulate that the user must have one or more tags:

Source https://stackoverflow.com/questions/64719412

QUESTION

How to include shell script suite in docker file

Asked 2020-Nov-06 at 00:24

I am trying to create a docker image for BBMAP (https://sourceforge.net/projects/bbmap/files/latest/download) shell script suite available online along with samtools and picard.jar. I was able to run samtools and picard, but for some reason I am not able to add bbmap below. Can someone please let me know what I am missing here?

I am trying to add shell scripts to bin to run them as executables. In my docker file below, this is where I need help:

...

ANSWER

Answered 2020-Nov-06 at 00:24

Earlier in your script, you run:

Source https://stackoverflow.com/questions/64706962

QUESTION

Docker image generating error for /usr/bin/java

Asked 2020-Nov-03 at 06:11

I am trying to run this docker image, but not sure why I am getting this error:

...

ANSWER

Answered 2020-Nov-03 at 06:11

Exit status 127 means no command found.

This is due to the java command in openjdk:8-jre not located in /usr/bin/java, see next:

Source https://stackoverflow.com/questions/64657384

QUESTION

Merge vcf files in snakemake

Asked 2020-Oct-21 at 15:30

After running the variant calling, I would like to merge only specific outputs as shown in d. This is giving me an error of missing input files. How to solve this?

...

ANSWER

Answered 2020-Oct-21 at 15:30

The output of varcall is

Source https://stackoverflow.com/questions/64465062

QUESTION

How to use singularity and conda wrappers in Snakemake

Asked 2020-Sep-22 at 23:02

TLDR I'm getting the following error:

The 'conda' command is not available inside your singularity container image. Snakemake mounts your conda installation into singularity. Sometimes, this can fail because of shell restrictions. It has been tested to work with docker://ubuntu, but it e.g. fails with docker://bash

I had created a Snakemake workflow and converted the shell: commands to rule-based package management via Snakemake wrappers: .

However, I ran into issues running this on HPC and one of the HPC support staff strongly recommended against using conda on any HPC system as:

"if the builder [of wrapper] is not super careful, dynamic libraries present in the conda environment that relies on the host libs (there are always a couple present because builder are most of the time carefree) will break. I think that relying on Singularity for your pipeline would make for a more robust system." - Anon

I did some reading over the weekend and according to this document, it's possible to combine containers with conda-based package management; by defining a global conda docker container and per-rule yaml files.

Note: In contrast to the example in the link above (Figure 5.4), which uses a predefined yaml and shell: command, here I've use conda wrappers which download these yaml files into the Singularity container (if I'm thinking correctly) so I thought should function the same - see the Note: at the end though...

Snakefile, config.yaml and samples.txt Snakefile ...

ANSWER

Answered 2020-Sep-22 at 15:02

TLDR:

fastqc singularity container used in qc rule likely doesn't have conda available in it, and this doesn't satisfy what snakemake's--use-conda expects.

Explanation:

You have singularity containers defined at two different levels - 1. global level that will be used for all rules, unless they are overridden at rule level; 2. per-rule level that will be used at the rule level.

Source https://stackoverflow.com/questions/64000711

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

Vulnerabilities

CVE-2017-16194 HIGH

picard is a micro framework. picard is vulnerable to a directory traversal issue, giving an attacker access to the filesystem by placing "../" in the url.

https://nodesecurity.io/advisories/436

https://github.com/JacksonGL/NPM-Vuln-PoC/blob/master/directory-traversal/picard

Install picard

You can download it from GitHub.
You can use picard like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: