Closed ubhuiyan closed 1 month ago
I have tried to create the datasets -- please check.
Here are some points:
Please assign the ticket back to me after you edit misc/ds2bco.json so that I can update the datasets
I have updated the misc/ds2bco.json. Please let me know if there's any issues.
I have updated the datasets, please check
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' human_proteoform_glycosylation_sites_carbbank.csv | head -2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"Q6P1J9-1" "G36855WW" "O-linked" "protein_xref_pubmed" "93364082" "protein_xref_glygen_ds" "GLY_001113"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' rat_proteoform_glycosylation_sites_carbbank.csv | head -2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"A6JX65-1" "G36855WW" "O-linked" "protein_xref_pubmed" "93364082" "protein_xref_glygen_ds" "GLY_001115"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' mouse_proteoform_glycosylation_sites_carbbank.csv | head
-2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"Q3UD01-1" "G99229VQ" "N-linked" "protein_xref_pubmed" "7496147" "protein_xref_glygen_ds" "GLY_001114"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' yeast_proteoform_glycosylation_sites_carbbank.csv | head
-2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"P0CW41-1" "G46565HP" "N-linked" "protein_xref_pubmed" "7496153" "protein_xref_glygen_ds" "GLY_001116"
Source file: downloads/carbbank/current/carbbank.csv
Mapping files: downloads/glytoucan/current/export/carbbank.tsv
Output file: *_proteoform_glyosylation_sites_carbbank.csv
The output file should have the following headers:
Organism Mapping:
See the chart below for instructions on mapping source fields to output (if any required fields are missing here, add them in with blank values):
O-linked if "O-linked glycopeptide" or "O-linked glycoprotein"
Example:
Input file
Output file