Implement version 1

[ReneRanzinger]

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:

1. Name of the original GWS file (only if -d is used)
2. Number of the sequence in the GWS file
3. GlyTouCan ID (only if -g is not used)
4. 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.

[senaarpinar]

add a column for errors into the excel sheet

[senaarpinar]

The first version is implemented