mdu-pytools 0.1.0

Small tools/scripts written in Python for MDU

MDU Python Tools

• MDU Python Tools
  • Background
  • Tools
    • merge-ngs-lanes
  • Development
    • Development environment

Background

Some simple tools in python for MDU

Tools

merge-ngs-lanes

Use it to correctly merge lanes from an Illumina run into the a single FASTQ.

Get help:

merge-ngs-lanes --help

Basic usage:

merge-ngs-lanes -i /path/to/fastq_folder -o /path/to/output > cmd.sh

Advanced usage:

You can split the output to muliple subfolders of the output folder by adding --subfolder to the command line. The option can be used multiple times, and takes two space separated values as input: path regex. The path gives a name of the subfolder in the output folder, and the regex expression determines which samples go in that subfolder.

For instance, the command below will split samples starting the NTC in to a subfolder called ntc, while all other samples will be added to a subfolder called data.

merge-ngs-lanes -i /path/to/fastq -o /path/to/output --subfolder 'data' '(?!NTC).*' --subfolder 'ntc' '(?<=NTC).*' > cmd.sh

Development

Development environment

To develop with the same environment use vagrant and virtualbox:

vagrant up
vagrant ssh

Once logged in to the VM, the shared folder is in /vagrant.