Note

download files and patial data: git fork https://github.com/faye-yang/BCB430.git
change file name and file path as needed in main and body function for all files as needed. Only ParsePassatotoOutput.py has use file path in the function body to check if a file exist.
most of the files are parsers, script files not in passatuto and sirius might need to change file path.
Passatuto2 and SIRIUS4 are in two docker containers

Data files

Target Library file: DDA_consensus_library_pos.tsv
DDA_decoy_library_reroot.txt: transition file for reroot method
DDA_decoy_library.txt: transition file for conditional peak method
decoy_library_reroot.tsv: decoy library for reroot method
conditionalPeak_library_decoy.tsv: decoy library for conditional peak method

Data file of passatuto2

contain all zip data files that is used for or outputed from passatuto2

txt file for sirius:Passatuto2/fragmentationTree
.Dot files from SIRUS:Passatuto2/tree_dot
parsed .Dot files from .Dot file for Passatuto: Passatuto2/TreeDir
source data from Passatuto2: Passatuto2/Data
parsed .ms file for RandomPeaks and conditionalPeak method: Passatuto2/data2
output data from reroot method from passatuto: Passatuto2/output_reroot
output data from conditional peak method from passatuto2: Passatuto2/output_conditionalPeak
dockerfile: a copy of docker file for building the docker image

tools using (softwares are not included in the github):

SIRIUS:a tool that construct a fragmentation tree, script.sh to run sirius

website: https://bio.informatik.uni-jena.de/software/sirius/

Passatuto2: a tool that construct decoy library using 4 methods,RandomPeaks, conditionalPeak, reroot, and Empirical-Bayes-

Approach(this appoarch can only support for the tool source data using method and database: MassBank,CosineDistance).
github: https://github.com/boecker-lab/passatuto

e.g. java -cp "lib/passatutto.jar:lib/json-1.0.jar:lib/commons-math3-3.4.1.jar:lib/trove4j-3.0.3.jar" DecoyDatabaseConstruction -target /data2 -out /outputRandom -method RandomPeaks -ppm 10 -ae 2

script directoy:

convert.py: a script from Prof. Hannes Rost that convert decoy library.

control.sh:example command and output from Prof. Hannes Rost for running the OpenSwath and pyprophet

script.sh: a bash script to run sirius. Note: it must in sirius/bin/ directory to work. the github version is just a copy. to run this file: cd sirius/bin/ then ./script.sh

library2ms.py: a parser script that has many parsers

goal:parse mass spectrometry library file (e.g.DDA_consensus_library_pos.tsv) to ms file for sirius and passatuto for RandomPeaks and conditionalPeak method and parse file from .dot to older version of SIRIUS .dot for reroot method.
function:

1.parseLibMs:parse mass spectrometry library file e.g.DDA_consensus_library_pos.tsv passatuto for RandomPeaks and conditionalPeak method.

Need: mass spectrometry library file

input: a line of the library file which contain infomation about molecule, that must contain: compound name, formula,parentmass
output: a ms file of such molecule

2.parseLibMsSirius:parse library file (e.g. DDA_consensus_library_pos.tsv) to ms file for sirius

input: a line of the library file which contain infomation about molecule, that must contain: compound name, formula,parentmass
output: a ms file of such molecule that contain only the parentmass and the intensity

3.formatSirius: parse file from .dot to older version of SIRIUS .dot for reroot method

input:a path to the dot file
output: a dot file in a older verison of SIRIUS dot file.

ParsePassatotoOutput.py: parse to the format that transition.py can recognize. Must run this before transition.py.

transition.py: a decoy transition library file. Need to concatenate with target library to work for Pyprophet and OpenSwath for all decoy libraries after running this function.

e.g. cat conditionalPeak_library_reroot.tsv ../DDA_consensus_library_pos.tsv >> conditionalPead_decoy.tsv .replace the file path as you need for all decoy library

insturction/work flow:

Passatuto2 example command: java -cp "lib/passatutto.jar:lib/json-1.0.jar:lib/commons-math3-3.4.1.jar:lib/trove4j-3.0.3.jar" DecoyDatabaseConstruction -target /data2 -out /outputRandom -method RandomPeaks -ppm 10 -ae 2 SIRIUS4 example command: sirius -f C20H19NO5 -2 demo-data/txt/chelidonine_msms2.txt demo-data/txt/chelidonine_msms2.txt SIRIUS4 example script:

random/conditional peak: Library file(DDA_consensus_library_pos.tsv)->ms file(Passatuto2/data2) ->run passatuto2 -> output file (output_conditionalPeak) reroot method: Library file(DDA_consensus_library_pos.tsv) -> txt file(Passatuto2/fragmentationTree) -> SIRIUS4 (output file:Passatuto2/tree_dot) --> parse dot file format(using formatSirius funtion of library2ms.py; output file:Passatuto2/TreeDir) -> output file( Passatuto2/output_reroot)

example fragmentation tree .dot file format

strict digraph {
v1 [label="C57H87O3\n819.6650 Da, 0.00 %\ncE: [10]\nScore: 1.0000"];
v2 [label="C6H13O3\n133.0863 Da, 72.59 %\ncE: [10]\nScore: -7.1438"];
v3 [label="C4H9O2\n89.0593 Da, 100.00 %\ncE: [10]\nScore: 14.4395"];
v4 [label="C6H13\n85.1005 Da, 29.18 %\ncE: [10]\nScore: 6.0633"];
v5 [label="C2H5O\n45.0334 Da, 41.80 %\ncE: [10]\nScore: 6.3635"];

v1 -> v2 [label="C51H74"];
v3 -> v5 [label="C2H4O"];

}

docker

ref tutorial: https://www.youtube.com/watch?v=FlSup_eelYE

dockerfile: https://docs.docker.com/engine/reference/builder/

To start:

docker build -t passatuto .

docker run -t passatuto /TreeDir /output_reroot Reroot

To stop/remove container:

docker stop passatuto-container

docker rm passatuto-container

Use docker (not deploy yet not test yet)