/data/shared/glygen/downloads/glytoucan/gtc_07_12_2022/README.txt

# retrieve current export from PyGly GitHub
$ wget https://github.com/glygen-glycan-data/PyGly/archive/refs/tags/GlyGen-GlycanData-Export-v1.11.0.zip

# unzip export folder
$ unzip GlyGen-GlycanData-Export-v1.11.0.zip

# move export folder to downloads, delete unused PyGly directory
$ mv PyGly-GlyGen-GlycanData-Export-v1.11.0/smw/glycandata/export/ /data/shared/glygen/downloads/glytoucan/gtc_07_12_2022/
$ rm -rf PyGly-GlyGen-GlycanData-Export-v1.11.0/
$ rm -rf GlyGen-GlycanData-Export-v1.11.0.zip

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# run unzip.sh program in new export folder
$ cd /data/shared/glygen/downloads/glytoucan/gtc_07_12_2022/export/ && bash /software/glygen/legacy/unzip.sh 

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# run glycan_images.sh program in new export folder
$ cd /data/shared/glygen/downloads/glytoucan/gtc_07_12_2022/export/ && bash /software/glygen/legacy/glycan_images.sh

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# convert byonic_glygen_human_nlinked.txt to byonic_glygen_human_nlinked.tsv where first column is GlyTouCanAccession and second column is Byonic

# print GlyTouCan Accession in first column and convert to .tsv
$ awk '{print $4"\t"$1,$2,$3}' byonic_glygen_human_nlinked.txt > byonic_glygen_human_nlinked.tsv

# remove comma at end of each row, save in place
$sed -i 's/,//' byonic_glygen_human_nlinked.tsv

#insert headers, save in place
$ sed -i '1i\GlyTouCanAccession\tByonic' byonic_glygen_human_nlinked.tsv