Java command line program with the following options:
-f
GWS file. Exactly one of -f, -j or -d must be present.
-d
Folder with GWS files. Exactly one of -f, -j or -d must be present.
-g
GlyTouCan ID generation. At least one of -g or -c must be present.
-c
Cartoon generation. At least one of -g or -c must be present.
-o
Output folder. Mandatory.
-j
Job file. Exactly one of -f, -j or -d must be present.
Program logic
Load the GWS sequences from the GWS file (-f) or from multiple GWS files (-d). Or retrieve the last job dump with -j
Generate the glycan cartoon (if -c is used)
Retrieve the GlyTouCan IDs (if -g is used). If necessary register them. Store the status for each structure (was already in GlyTouCan, newly submitted for registration, newly registered). If the last status was "newly submitted for registration" and a -j rerun shows that it is now in GlyTouCan the status changes to "newly registered".
Generate the Excel output in the output folder (see below)
Serialize the job into a json file in the output folder
Output
Excel file with the following columns:
Name of the original GWS file (only if -d is used)
Number of the sequence in the GWS file
GlyTouCan ID (only if -g is not used)
Glycan Cartoon (only if -c is not used)
Job File
This file contains the last status of the current job. It has a list of input files. With each file having a list of glycans. Each glycan has a GWS sequences (other sequences such as GlycoCT and WURCS as needed), the last status from the GlyTouCan registration.
Java command line program with the following options:
-f
GWS file. Exactly one of -f, -j or -d must be present.-d
Folder with GWS files. Exactly one of -f, -j or -d must be present.-g
GlyTouCan ID generation. At least one of -g or -c must be present.-c
Cartoon generation. At least one of -g or -c must be present.-o
Output folder. Mandatory.-j
Job file. Exactly one of -f, -j or -d must be present.Program logic
-f
) or from multiple GWS files (-d
). Or retrieve the last job dump with-j
-c
is used)-g
is used). If necessary register them. Store the status for each structure (was already in GlyTouCan, newly submitted for registration, newly registered). If the last status was "newly submitted for registration" and a-j
rerun shows that it is now in GlyTouCan the status changes to "newly registered".Output Excel file with the following columns:
Job File This file contains the last status of the current job. It has a list of input files. With each file having a list of glycans. Each glycan has a GWS sequences (other sequences such as GlycoCT and WURCS as needed), the last status from the GlyTouCan registration.