Small tools/scripts written in Python for MDU
MDU Python Tools
- MDU Python Tools
Some simple tools in python for MDU
Use it to correctly merge lanes from an Illumina run into the a single FASTQ.
mdu-merge-ngs-lanes -i /path/to/fastq_folder -o /path/to/output > cmd.sh
You can split the output to muliple subfolders of the output folder by adding
to the command line. The option can be used multiple times, and takes two space separated values as input:
path gives a name of the subfolder in the output folder, and the
determines which samples go in that subfolder.
For instance, the command below will split samples starting the NTC in to a subfolder called
while all other samples will be added to a subfolder called
mdu-merge-ngs-lanes -i /path/to/fastq -o /path/to/output --subfolder 'data' '(?!NTC).*' --subfolder 'ntc' '(?<=NTC).*' > cmd.sh
Use to it to upload FASTQ data to NCBI SRA.
Requires a file with tab-separated values of
MDU ID and
AUSMDUID. For example:
Usage: mdu-sra-upload [OPTIONS] ISOLATES Options: -f, --folder TEXT Folder on NCBI to upload. Used to find the reads when submitting via the SRA portal. [default: mdu] -r, --reads-folder TEXT Where reads are located (uses MDU_READS env variable if available). -k, --ascp-key TEXT Path to ascp ssh upload key (uses ASCP_UPLOAD_KEY env variable if available). This can be obtained from the SRA Submission Portal. -s, --sra-subfolder TEXT SRA subfolder owned by you where data will copied to (uses SRA_SUBFOLDER env variable is available). --help Show this message and exit.
cd /path/for/upload # copy paste isolates.txt mdu-sra-uploads isolates.txt # when completing the submission, search for pre-uploaded files in the folder called mdu
Environmental variables that can be used to set options
MDU_READS: full path to where FASTQ data is stored
ASCP_UPLOAD_KEY: full path to where your Aspera NCBI upload key is located (obtain one from the SRA submission portal under the Aspera command line instructions)
SRA_FOLDER: path to your folder at SRA. Usually composed by your
To develop with the same environment use
vagrant up vagrant ssh
Once logged in to the VM, the shared folder is in
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