fuc 0.2.0

Frequently used commands in bioinformatics

Introduction

The main goal of the fuc package is to wrap some of the most frequently used commands in the field of bioinformatics into one place.

You can use fuc for both command line interface (CLI) and application programming interface (API) whose documentations are available at Read the Docs.

Your contributions (e.g. feature ideas, pull requests) are most welcome.

Author: Seung-been “Steven” Lee

Email: [e-mail]

License: MIT License

Examples

To merge VCF files with CLI:

$ fuc vfmerge 1.vcf 2.vcf 3.vcf > merged.vcf

To filter a VCF file based on a BED file using API:

from fuc import pyvcf
vf = pyvcf.read_file('original.vcf')
filtered_vf = vf.filter_bed('targets.bed')
filtered_vf.to_file('filtered.vcf')

Required Packages

The following packages are required to run fuc:

numpy
pandas
pyranges

Getting Started

There are various ways you can install fuc. The easiest one would be to use pip:

$ pip install fuc

Above will automatically download and install all the dependencies as well.

Alternatively, you can clone the GitHub repository and then install fuc this way:

$ git clone https://github.com/sbslee/fuc
$ cd fuc
$ pip install .

Above will also allow you to install a development version that’s not available in PyPI.

For getting help on CLI:

$ fuc -h
usage: fuc [-h] [-v] COMMAND ...

positional arguments:
  COMMAND        name of the command
    bfintxn      [BED] find intersection of two or more BED files
    bfsum        [BED] summarize a BED file
    dfmerge      [TABLE] merge two text files
    dfsum        [TABLE] summarize a text file
    fuccompf     [FUC] compare contents of two files
    fucexist     [FUC] check whether files/dirs exist
    qfcount      [FASTQ] count sequence reads in FASTQ files
    qfsum        [FASTQ] summarize a FASTQ file
    vfmerge      [VCF] merge two or more VCF files

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  show the version number and exit

For getting help on a specific command (e.g. vfmerge):

$ fuc vfmerge -h

Below is the list of submodules available in API:

• common : The common submodule is used by other fuc submodules such as pyvcf and pybed. It also provides many day-to-day actions used in the field of bioinformatics.

• pybed : The pybed submodule is designed for working with BED files. It implements pybed.BedFrame which stores BED data as a pyranges.PyRanges to allow fast computation and easy manipulation.

• pyfq : The pyfq submodule is designed for working with FASTQ files (both zipped and unzipped). It implements pyfq.FqFrame which stores FASTQ data as a pandas.DataFrame to allow fast computation and easy manipulation.

• pyvcf : The pyvcf submodule is designed for working with VCF files (both zipped and unzipped). It implements pyvcf.VcfFrame which stores VCF data as a pandas.DataFrame to allow fast computation and easy manipulation.

• snpeff : The snpeff submodule is designed for parsing VCF annotation data from the SnpEff program. It should be used with pyvcf.VcfFrame.

For getting help on a specific module (e.g. pyvcf):

from fuc import pyvcf
help(pyvcf)