Small tools/scripts written in Python for MDU
Project description
MDU Python Tools
Background
Some simple tools in python for MDU
Tools
mdu-merge-ngs-lanes
Use it to correctly merge lanes from an Illumina run into the a single FASTQ.
Get help:
mdu-merge-ngs-lanes --help
Basic usage:
mdu-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
.
mdu-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
.
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