alastair-droop/misc-tools

Miscellaneous Bioinformatics Scripts

Miscellaneous Bioinformatics Tools

This is a set of miscellaneous bioinformatics tools.

cutadapt-stats

This script extracts cutadapt statistics from from a set of cutadapt log files and outputs the data in a tabular format.

Usage

cutadapt-stats [-h] [-v] [-n] [-c] <filename> [<filename> ...]

positional arguments:

• <filename> cutadapt log file(s) to process

optional arguments:

• -h, --help show this help message and exit
• -v, --version show program's version number and exit
• -n, --no-header suppress column headers
• -c, --csv output data as CSV (ignores -n)

For each log file, either a single entry (if it was a single pair) or two entries (if it was a pair) are returned. The output columns are:

• id : The log file ID
• file : The log file
• type : The type
• r_total : Total reads processed
• b_total : Total bases processed
• r_out : Total reads passing filter
• b_out : Total bases passing filter
• r_adapt : Number of reads with adapter contamination
• r_rm_long : Reads rejected as too long (flag -M)
• r_rm_short: Reads rejected as too short (flag -m
• r_rm_other: Reads rejected for any other reason
• b_rm_adapt: Bases trimmed as adapter
• b_rm_qual : Bases trimmed as low quality (flag -q)
• b_rm_other: Reads trimmed for any other reason

Installation

The script should be executable on any system that has python3 installed. On python version <3.2, the argparse package is not included in the standard library and must be separately installed.

fastqc-extract

This script processes a set of FastQC ZIP files to produce summary tables.

Usage

fastqc-extract [-h] [-v] [-c] [-e] [-s] <module> <filename> [<filename> ...]

positional arguments:

• <module> The module
• <filename> FastQC ZIP file(s) to process

optional arguments:

• -h, --help show this help message and exit
• -v, --version show program's version number and exit
• -c, --csv return CSV-formatted data
• -e, --header include header in output
• -s, --summary generate module summary

Modules

Modules can be provided by name or by number. Non-standard modules must be supplied by name:

Number	Name
1	Basic Statistics
2	Per base sequence quality
3	Per tile sequence quality
4	Per sequence quality scores
5	Per base sequence content
6	Per sequence GC content
7	Per base N content
8	Sequence Length Distribution
9	Sequence Duplication Levels
10	Overrepresented sequences
11	Adapter Content
12	Kmer Content

Installation

The script should be executable on any system that has python3 installed. On python version <3.2, the argparse package is not included in the standard library and must be separately installed.