Comments (2)
pbnjay
commented on September 18, 2024
Hi Lukas!
Sorry, the local file option is a bit rough / not well documented. It's still expecting a protein reference ID, although it will replace that data with yours. So you need one of the three options here:
{-Q UNIPROT_DB IDENTIFER | -U UNIPROT_ID | GENE_SYMBOL}
You may want to use -o=output.svg to be sure where your output is going too.
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leiendeckerlu
commented on September 18, 2024
Hey!
super nice, that fixed it - I did it like this now:
./lollipops -l="./E6.json" -legend -f="/Library/Fonts/Arial Unicode.ttf" -o="json.svg" RB1
It's still a bit confusing that the tool outputs the RB1 associated stuff:
--> SNIP
HGNC Symbol: RB1
Uniprot returned 155 hits for your gene symbol 'RB1':
Entry Entry name Status Gene names Organism
P06400 RB_HUMAN reviewed RB1 Homo sapiens (Human)
Q8TDY2 RBCC1_HUMAN reviewed RB1CC1 KIAA0203 RBICC Homo sapiens (Human)
P42701 I12R1_HUMAN reviewed IL12RB1 IL12R IL12RB Homo sapiens (Human)
Q8IUH3 RBM45_HUMAN reviewed RBM45 DRB1 DRBP1 Homo sapiens (Human)
Q01094 E2F1_HUMAN reviewed E2F1 RBBP3 Homo sapiens (Human)
O75832 PSD10_HUMAN reviewed PSMD10 Homo sapiens (Human)
Q9NY61 AATF_HUMAN reviewed AATF CHE1 DED HSPC277 Homo sapiens (Human)
Q14209 E2F2_HUMAN reviewed E2F2 Homo sapiens (Human)
Q9UBU8 MO4L1_HUMAN reviewed MORF4L1 MRG15 FWP006 HSPC008 HSPC061 PP368 Homo sapiens (Human)
--> SNAP
Thanks for your help & very nice tool!
Lukas
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Related Issues (20)
- uniprot error: 400 Bad Request HOT 6
- integer divide by zero using the -U option HOT 4
- error: no font loaded - cannot make PNG! HOT 1
- Uniprot ID of gene isoform HOT 4
- update Pfam links HOT 1
- Examples fail, uniprot error: 400 Bad Request. Error in UniProt ID lookup? HOT 12
- Lollipops go function shows "undefined: data.GetGraphicData"
- pfam certificate has expired or is not yet valid: HOT 4
- ./main.go:218:8: undefined: createOutput HOT 1
- panic: runtime error: index out of range [2] with length 0 HOT 3
- Avoiding Overlapping Text/ Changing Height of plot HOT 2
- pfam error: 403 forbidden
- Pfam vs InterPro: TP53 HOT 1
- can’t be opened because Apple cannot check it for malicious software HOT 1
- can not find the output file HOT 1
- invalid character '<' looking for beginning of value HOT 1
- Feature request: Toggle for no. of mutations as lollipop height.
- Change display
- Website app appears to be broken? HOT 1
- InterPro Error:404 not Found HOT 1
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