parallel-fastq-dump | parallel fastq-dump wrapper | Genomics library

by rvalieris Python Version: 0.6.5 License: MIT

X-Ray Key Features Code Snippets(1)Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | parallel-fastq-dump Summary

parallel-fastq-dump is a Python library typically used in Artificial Intelligence, Genomics applications. parallel-fastq-dump has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install parallel-fastq-dump' or download it from GitHub, PyPI.

parallel fastq-dump wrapper

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Quality

Security

License

Reuse

Support

parallel-fastq-dump has a low active ecosystem.

It has 224 star(s) with 28 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 5 open issues and 43 have been closed. On average issues are closed in 27 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of parallel-fastq-dump is 0.6.5

Quality

parallel-fastq-dump has 0 bugs and 0 code smells.

Security

parallel-fastq-dump has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

parallel-fastq-dump code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

parallel-fastq-dump 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

parallel-fastq-dump releases are available to install and integrate.

Deployable package is available in PyPI.

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

parallel-fastq-dump saves you 8 person hours of effort in developing the same functionality from scratch.

It has 24 lines of code, 0 functions and 1 files.

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

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parallel-fastq-dump Key Features

No Key Features are available at this moment for parallel-fastq-dump.

parallel-fastq-dump Examples and Code Snippets

Snakemake - How to use every line of input file as wildcard

Python

Lines of Code : 12

License : Strong Copyleft (CC BY-SA 4.0)

Copy

rule all:
    input: expand("out/{sample}_fastq.gz", sample=samples)

rule download_sample:
    output: 
        "out/{sample}_fastq.gz"
    params:
        outdir = "out",
        threads = 16
    priority:85
    shell:"parallel-fastq-dum

Community Discussions

Trending Discussions on parallel-fastq-dump

How to handle mutliple output filename conventions with Snakemake

Snakemake - How to use every line of input file as wildcard

QUESTION

How to handle mutliple output filename conventions with Snakemake

Asked 2019-Jun-16 at 02:44

I have a scenario where the output filenames of a program are not consistent and hence I am having difficulty defining snakemake rules.

I am retrieving data from SRA and I do not know if the program will return 1 file or 2 files

Here are the 2 situations :

Situation 1

...

ANSWER

Answered 2019-Jun-15 at 08:08

One solution may be to touch a file when fastq-dump has completed and use that file as input to the other rules.

In the case you posted, the name of the actual fastq files can be reconstructed from the SRR id and you can tell whether you have 1 or 2 fastq files based on the suffix _1.fastq.gz or _2.fastq.gz.

Here's an example:

Source https://stackoverflow.com/questions/56599704

QUESTION

Snakemake - How to use every line of input file as wildcard

Asked 2019-Jun-11 at 14:59

I am pretty new to using Snakemake and I have looked around on SO to see if there is a solution for the below - I am almost very close to a solution, but not there yet.

I have a single column file containing a list of SRA ids and I want to use snakemake to define my rules such that every SRA id from that file becomes a parameter on command line.

...

ANSWER

Answered 2019-Jun-11 at 06:42

The first solution could be to use the run: section of the rule instead of the shell:. This allows you to employ python code:

Source https://stackoverflow.com/questions/56535751

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

Vulnerabilities

No vulnerabilities reported

Install parallel-fastq-dump

You can install using 'pip install parallel-fastq-dump' or download it from GitHub, PyPI.
You can use parallel-fastq-dump 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 .

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