Scripts for making the use of X! Tandem easier.
Written by Adam Schaal, UC Davis Bioinformatics Core
Revised by Kristen Beck, UC Davis Genome Center
usage: generate_tandem_inputs.py [-h] --mzml MZML [MZML ...] --directory DIRECTORY --default_file DEFAULT_FILE --fasta_file FASTA_FILE [--threads THREADS] [--resources RESOURCES] [--email EMAIL]
Generates input.xml, taxonomy.xml (fasta database info), and qsub bash script to run xtandem from Genome Center cluster
optional arguments:
-h, --help
show this help message and exit
--mzml MZML [MZML ...]
An mzML file path. May use wildcards to use multiple
files, such as *.mzML (optionally .dta files are also
accepted and are used when running X!Tandem on unmatched
spectra exported from Scaffold)
--directory DIRECTORY
The of the directory to output all files to. The
directory will be made if it does not exist.
--default_file DEFAULT_FILE
The path to the default xml file.
--fasta_file FASTA_FILE
Fasta file
--threads THREADS
The number of threads to run for each X! Tandem job
--resources RESOURCES
The requested resources for the job
--email EMAIL
Email address for notification whe job begins, ends,
or aborts
Note: Python version 2.7 or greater is required. It can be loaded with the following command: module load python/2.7.8
Example usage for generic project python generate_tandem_inputs.py --mzml /full/path/to/spectra/*.mzML --directory /full/path/to/best_run_ever --default_file /share/milklab/proteomics/Tools/XTandem/tandem-linux-15-04-01-1/bin/default_input.xml --fasta_file /full/path/to/example.fasta --threads 2 --resources h_vmem=2g --email [email protected]
Once the script has completed running, source the tandem_qsub.bash script to submit the job.
Example usage for milk proteomics project: Note use of "default file" that matches wetlab method python generate_tandem_inputs.py --mzml /share/milklab/proteomics/Spectra/Human/*.mzML --directory /share/milklab/proteomics/run_XTandem/best_milk_ever --default_file /share/milklab/proteomics/Tools/XTandem/tandem-linux-15-04-01-1/bin/methods_matching_wetlab/qexactive_input_wPNGaseF.xml --fasta_file /share/milklab/proteomics/FASTA/Uniprot_Human-decoy+cRAP.fasta --threads 2 --resources h_vmem=2g --email [email protected]
Once the script has completed running, source the tandem_qsub.bash script to submit the job.