Rationale
Use Python to make your experience with Waters' Symphony Pipeline a much nicer experience. Otherwise said, add some synthactic sugar to Waters. In my country this results in Vodkas.
Installation
pip install git+https://github.com/MatteoLacki/vodkasUsage
Here is an examplary use. Be sure to set up the remote disks before-hand and make sure that all folders have proper, most lenient access privileges.
from pathlib import Path
from vodkas import apex3d, peptide3d, iadbs
from vodkas.fs import cp
raw = Path("C:/ms_soft/MasterOfPipelines/RAW/O1903/O190302_01.raw")
temp = Path("C:/Symphony/Temp/test")
apexOutPath, apex_proc = apex3d(raw, temp, write_binary=True, capture_output=True)
apexOutBIN = apexOutPath.with_suffix('.bin')
pep3dOutPath, pep_proc = peptide3d(apexOutBIN, temp,
write_binary=True,
min_LEMHPlus=350.0,
capture_output=True)
pep3dOutXML = pep3dOutPath.with_suffix('.xml')
iadbsOutPath, iadbs_proc = iadbs(pep3dOutXML, temp,
fasta_file="C:/Symphony/Search/human.fasta",
parameters_file="C:/Symphony/Search/251.xml",
capture_output=True)Best Regards, Matteo Lacki
