PyVCF | A Variant Call Format reader for Python

by jdoughertyii Python Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions(7)Vulnerabilities Install Support

kandi X-RAY | PyVCF Summary

PyVCF is a Python library. PyVCF has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However PyVCF build file is not available. You can download it from GitHub.

A Variant Call Format reader for Python.

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Quality

Security

License

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Support

PyVCF has a low active ecosystem.

It has 62 star(s) with 190 fork(s). There are 7 watchers for this library.

It had no major release in the last 6 months.

There are 0 open issues and 6 have been closed. On average issues are closed in 203 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of PyVCF is current.

Quality

PyVCF has 0 bugs and 3 code smells.

Security

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

PyVCF code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

PyVCF 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

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

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

PyVCF saves you 107 person hours of effort in developing the same functionality from scratch.

It has 271 lines of code, 23 functions and 1 files.

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

Top functions reviewed by kandi - BETA

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

Parse a string into a dict
Main function .
Parses the vcf file .
Parse the next record .
Read format from format_string .
Read the info from a string .
Read a filter from a string .
Call the function
Get the docstring of the function .
Return the docstring of the function .

Get all kandi verified functions for this library.

PyVCF Key Features

No Key Features are available at this moment for PyVCF.

PyVCF Examples and Code Snippets

No Code Snippets are available at this moment for PyVCF.

Community Discussions

Trending Discussions on PyVCF

Slow python code to parse VCF file and insert in database

Dataflow error: TypeError: request() got an unexpected keyword argument 'data', how can I fix my deps?

IndexError: index 261861 is out of bounds for axis 0 with size 169567

ImportError phonenumbers with google cloud dataflow python

How to get the result of an SQL query from Big Query in Airflow?

Python to print a returned value can be either a list or a int

Anaconda, Python package install through pip not working, Linux

QUESTION

Slow python code to parse VCF file and insert in database

Asked 2019-Dec-13 at 14:33

I have the following code which is written to parse VCF (Variant call format) file:

Python code:

...

ANSWER

Answered 2019-Dec-12 at 11:36

INSERT INTO XXX (column list) VALUES (values list) is not the optimal I replace this by syntax "INSERT INTO XXX VALUES", formatted list

It improve drastically performances 10 minutes ==> under 15 sec

(I did it in python 3.7.5)

Source https://stackoverflow.com/questions/59200451

QUESTION

Dataflow error: TypeError: request() got an unexpected keyword argument 'data', how can I fix my deps?

Asked 2019-May-01 at 00:39

I am working on a Google Dataflow project and here are the requirements for the project:

...

ANSWER

Answered 2019-May-01 at 00:39

It's possible that a square bracket is a special character for your shell. You can try pip install 'apache-beam[gcp]'.

Source https://stackoverflow.com/questions/55930301

QUESTION

IndexError: index 261861 is out of bounds for axis 0 with size 169567

Asked 2018-Jul-25 at 15:52

I am a beginner in programming and I have the following problem: I want to write a definition where I create an empty matrix with the data of the chosen chromosome out of a vcf-file (with pyvcf).The empty matrix is created correctly.

IndexError: index 261861 is out of bounds for axis 0 with size 169567

But this error above occurs if I try the second chromosome as input. The first chromosome ends at index 262860, this is why I think somehow it want to place the data of the line in this line of the matrix, but I do not understand why!

This is my code:

...

ANSWER

Answered 2018-Jul-25 at 15:52

You are adding up z for every line in vcf_reader, while you only want to do that if the chromosome you want is identified.

Simply putting z=z+1 inside the if statement should do the trick like so:

Source https://stackoverflow.com/questions/51522878

QUESTION

ImportError phonenumbers with google cloud dataflow python

Asked 2018-Jun-20 at 19:56

I am trying to do a relatively simple import of the module phonenumbers in Python.

I have tested the module on a seperate python file without any other imports and it works completely fine.

These are the packages I have installed:

...

ANSWER

Answered 2018-Jun-18 at 23:04

It may be that Dataflow is not receiving the file with the extra dependencies of your pipeline. To install them, you'd do this:

Source https://stackoverflow.com/questions/50918217

QUESTION

How to get the result of an SQL query from Big Query in Airflow?

Asked 2018-Apr-03 at 07:41

Using Airflow I want to get the result of an SQL Query fomratted as a pandas DataFrame.

...

ANSWER

Answered 2018-Apr-03 at 07:41

Another possible way would be to use the pandas Big Query connector.

Source https://stackoverflow.com/questions/49619897

QUESTION

Python to print a returned value can be either a list or a int

Asked 2017-Dec-14 at 03:24

I am using pyVCF to read a VCF file, and the returned sample['AD'] can either be a list like [8, 14] or an int like 5.

If I use ','.join(map(str,sample['AD'])), it will stop at int returns as "TypeError: 'int' object is not iterable".

How can I write it to print it in both situations?

Reply to the comment:

Just normal code. But the VCF file come with two kinds of AD.

...

ANSWER

Answered 2017-Dec-13 at 13:50

Check if the result is instance of list or integer

Source https://stackoverflow.com/questions/47794440

QUESTION

Anaconda, Python package install through pip not working, Linux

Asked 2017-Sep-06 at 17:06

I am having issues installing packages using pip. When installing packages through conda from within my environment it works fine however when trying to install through pip I continue receiving the ImportError: No Module named X.

The packages I am trying to install are a group of packages that are not apart of the conda distribution.

Example

...

ANSWER

Answered 2017-Sep-06 at 13:28

try this first..

$ python3

Source https://stackoverflow.com/questions/46076110

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

Vulnerabilities

No vulnerabilities reported

Install PyVCF

You can download it from GitHub.
You can use PyVCF 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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