Build [https://www.ebi.ac.uk/seqdb/confluence/display/UniProt/GlyGen+Mapping+production]
> Run GetGlygenCanonicals to generate 12 isoform-canonical-sequence mapper files from swpfly
> UP000008095.tsv is non reference proteome, has only one sequence. If sequence changes, update it manually
> copy mapper_files to to /nfs/ftp/public/contrib/glygen/mapper_files/
> start docker desktop & login
> goto project command line eg: on windows- cd C:\Users\pvasudev\IdeaProjects\glygen.mapping
> mvn package
> start docker desktop & sign-in
> docker build -t mapper-java-jar:basic .
> docker tag mapper-java-jar:basic ebiglygen/mapper-java-jar:basic
> docker push ebiglygen/mapper-java-jar:basic
> docker run -v C:\temp\glygen\:/input ebiglygen/mapper-java-jar:basic


tickets: glygener/glygen-issues#1012; #1624, #560
Note:
Warning warning only for valid invalid input aa. Mapping is done. Only one warning message
> incorrect input aa' for invalid input aa in warning column

Error is when mapping can't be done. Four error messages
[error ondition - error message]
> invalid accession - invalid glygen accession
> missing input aa position - input position missing
> invalid input position (-ve or zero or non-integer) - invalid input position <aa_pos>
> invalid input position (pos > seq length) - input position <aa_pos> greater than sequence length

Invalid accession could be due to
syntax invalid : can be done regexp check
correct syntax, but accession not in uniprotkb eg: P05067-33 : can be done by uniprot api call, but will slow down tool massively
correct syntax, not belong to 13 glygen taxids : using uniprot api identify taxid of valid accession, check if it is one of glygen species, slows down the tool
correct syntax, belongs to 13 taxdis, but not in reference proteome : can be done having list of all uniprot accessions of glygen species