Sequence_Cleaner: Remove Duplicate Sequences, Short Sequences, etc

WARNING:

I originally created this script using Biopython back in the day, and recently I decided to re-write using Pysam and Python 3. I hope you enjoy it.

• Installation
  • dependencies
  • git
• Usage

Installation

Dependencies

• Python 3.6
• Setuptools 36.0.1
• Pysam 0.15.3

Git

# these steps should install the dependencies

# clone repo
git clone git@github.com:metageni/Sequence-Cleaner.git

# install tool
cd Sequence-Cleaner && pip install -U -r requirements.txt && python setup.py install

Usage

usage: sequence_cleaner [-h] [-v] -q QUERY -o OUTPUT_DIRECTORY
                        [-ml MINIMUM_LENGTH] [-mn PERCENTAGE_N]
                        [--keep_all_duplicates] [--remove_ambiguous] [-l LOG]

Sequence Cleaner: Remove Duplicate Sequences, etc

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -q QUERY, --query QUERY
                        Path to directory with FAST(A/Q) files
  -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
                        Path to output files
  -ml MINIMUM_LENGTH, --minimum_length MINIMUM_LENGTH
                        Minimum length allowed (default=0 - allows all the
                        lengths)
  -mn PERCENTAGE_N, --percentage_n PERCENTAGE_N
                        Percentage of N is allowed (default=100)
  --keep_all_duplicates
                        Keep All Duplicate Sequences
  --remove_ambiguous    Remove any sequence with ambiguous bases
  -l LOG, --log LOG     Path to log file (Default: STDOUT).

example > sequence_cleaner -q INPUT -o OUTPUT