NA12878 | Data and analysis for NA12878 genome on nanopore | Genomics library

by nanopore-wgs-consortium Python Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | NA12878 Summary

NA12878 is a Python library typically used in Artificial Intelligence, Genomics, Docker applications. NA12878 has no bugs, it has no vulnerabilities and it has low support. However NA12878 build file is not available and it has a Non-SPDX License. You can download it from GitHub.

Data and analysis for NA12878 genome on nanopore

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Quality

Security

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Support

NA12878 has a low active ecosystem.

It has 344 star(s) with 88 fork(s). There are 51 watchers for this library.

It had no major release in the last 6 months.

There are 40 open issues and 43 have been closed. On average issues are closed in 60 days. There are 5 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of NA12878 is current.

Quality

NA12878 has 0 bugs and 0 code smells.

Security

NA12878 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

NA12878 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

NA12878 has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

NA12878 releases are not available. You will need to build from source code and install.

NA12878 has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions are not available. Examples and code snippets are available.

NA12878 saves you 363 person hours of effort in developing the same functionality from scratch.

It has 867 lines of code, 29 functions and 9 files.

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

Top functions reviewed by kandi - BETA

kandi has reviewed NA12878 and discovered the below as its top functions. This is intended to give you an instant insight into NA12878 implemented functionality, and help decide if they suit your requirements.

Read data from a bulk summary file
Create figure
Read data from a file
Return a dict of dtype dtype dtype dtype
Update the figure
Given a variant line and a variant file return the genes and spec
Uniq a sequence
Calculate genes for a block - specific variant
Write bulk files
Smooth the mean of an array
Creates a fasta read file from a bulk read file
Argument parser
Convert a sequence of reads to bam
Create figure plot
Concatenate multiple input files into a pandas dataframe
Convert a bam file into a header
Update toggle
Update scale
Update the file
Prints message to stderr

Get all kandi verified functions for this library.

NA12878 Key Features

No Key Features are available at this moment for NA12878.

NA12878 Examples and Code Snippets

No Code Snippets are available at this moment for NA12878.

Community Discussions

Trending Discussions on NA12878

Extracting lines of text depending on the len() of a particular column

splitCsv then map a list of URLs in Nextflow

Unable to use rdd.toDF() but spark.createDataFrame(rdd) Works

QUESTION

Extracting lines of text depending on the len() of a particular column

Asked 2019-Feb-27 at 16:32

I'm trying to write a simple script to extract particular data from a VCF file, which displays variants in genome sequences.

The script needs to extract the header from the file, as well as SNVs while omitting any indels. Variants are displayed in 2 columns, the ALT and REF. Each column is separated by white space. Indels will have 2 characters in the ALT or REF, SNVs will always have 1.

What I have so far extracts the headers (which always begin with ##), but not any of the variant data.

...

ANSWER

Answered 2019-Feb-21 at 16:37

original_file = open('NA12878.vcf', 'r')
extracted_file = open('NA12878_SNV.txt', 'w+')
i=0

for line in original_file:
    if '##' in line:
        extracted_file.write(line)
    else:
        ref = line.split('  ')[3]
        alt = line.split('  ')[4]
        if len(ref) == 1 and len(alt) == 1:
            extracted_file.write(line)

# Extract SNVs while omitting indels 
# Indels will have multiple entries in the REF or ALT column
# The ALT and REF columns appear at position 4 & 5 respectively

original_file.close()
extracted_file.close()

Source https://stackoverflow.com/questions/54811052

QUESTION

splitCsv then map a list of URLs in Nextflow

Asked 2018-Nov-13 at 16:26

I am trying to take the GIAB data index files (which are CSVs), and download each file in Nextflow. I think I have the general structure right, but when I run nextflow run file.nf nothing happens.

...

ANSWER

Answered 2018-Nov-13 at 16:26

It's need to map the fastq path string to a file object using the file function e.g.:

Source https://stackoverflow.com/questions/53277369

QUESTION

Unable to use rdd.toDF() but spark.createDataFrame(rdd) Works

Asked 2017-May-07 at 03:07

I have an RDD of the form RDD[(string, List(Tuple))], like below:

...

ANSWER

Answered 2017-May-06 at 11:59

toDF method is executed under SparkSession in and SQLContex in 1.x version. So

Source https://stackoverflow.com/questions/43810603

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

Vulnerabilities

No vulnerabilities reported

Install NA12878

You can download it from GitHub.
You can use NA12878 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.