uniprot error: 400 Bad Request

[GKok]

Hi!

I've been using your tool for quite some time to visualize mutation locations.

However, I now receive an error when using the tool.

./lollipops -labels -w=1000 VARS1     

shows

HGNC Symbol:  VARS1
uniprot error: 400 Bad Request

Any idea how to fix this?

[mreyer93]

Bumping the above comment because I received the same error, regardless of the HGNC Symbol input

[pbnjay]

Hmm it looks like uniprot has changed their ID translation service again…

I’ll check what I can do, but in the meantime I believe you can use the -U option instead of the symbol: -U P26640

[mreyer93]

Looks like there is some progress using the -U option (I no longer get "uniprot error: 400 Bad request"), but I now see the following after entering the Uniprot ID for TP53, which produces an empty .png:

Gene Symbol: TP53B_HUMAN Drawing diagram to test.png panic: runtime error: integer divide by zero

goroutine 1 [running]: github.com/golang/freetype/truetype.mulDiv(...) /Users/jeremy/src/github.com/golang/freetype/truetype/hint.go:1729 github.com/golang/freetype/truetype.(hinter).move(0xc001c17390, 0xc001e1200c, 0x100000140) /Users/jeremy/src/github.com/golang/freetype/truetype/hint.go:1469 +0x1cf github.com/golang/freetype/truetype.(hinter).run(0xc001c17390, 0xc00018881c, 0x24b5, 0x15aab9c, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...) /Users/jeremy/src/github.com/golang/freetype/truetype/hint.go:706 +0x36bd github.com/golang/freetype/truetype.(hinter).init(0xc001c17390, 0xc00000c1e0, 0x300, 0x268, 0x4d) /Users/jeremy/src/github.com/golang/freetype/truetype/hint.go:158 +0x2e5 github.com/golang/freetype/truetype.(GlyphBuf).Load(0xc001c17300, 0xc00000c1e0, 0x3000000300, 0x2, 0xc001c14800, 0xc001dba000) /Users/jeremy/src/github.com/golang/freetype/truetype/glyph.go:98 +0x310 github.com/golang/freetype/truetype.(face).GlyphBounds(0xc001c14800, 0xc00000004d, 0x13ec580, 0xc001c14800, 0x409668ba2e8ba2e8) /Users/jeremy/src/github.com/golang/freetype/truetype/face.go:322 +0x6e github.com/joiningdata/lollipops/drawing.(diagram).png(0xc0000870e0, 0x13e5a40, 0xc0000100a8) /Users/jeremy/src/github.com/joiningdata/lollipops/drawing/png.go:161 +0x81e github.com/joiningdata/lollipops/drawing.(*Settings).DrawPNG(0x15ee940, 0x13e5a40, 0xc0000100a8, 0x4052000000000000, 0xc0000b8060, 0x1, 0x1, 0xc000087020) /Users/jeremy/src/github.com/joiningdata/lollipops/drawing/png.go:61 +0x139 github.com/joiningdata/lollipops/drawing.DrawPNG(...) /Users/jeremy/src/github.com/joiningdata/lollipops/drawing/png.go:37 main.createOutput(0x2057dd955, 0x8, 0xc000087020, 0xc0000b8060, 0x1, 0x1, 0x0, 0x0) /Users/jeremy/src/github.com/joiningdata/lollipops/output.go:22 +0x1c1 main.main() /Users/jeremy/src/github.com/joiningdata/lollipops/main.go:217 +0x618

[pbnjay]

@mreyer93 moving that to a separate issue as it seems unrelated

[GKok]

Hmm it looks like uniprot has changed their ID translation service again…

I’ll check what I can do, but in the meantime I believe you can use the -U option instead of the symbol: -U P26640

Apologies for the late reply - but this workaround works :-)

[chengxc032403]

Hi!

I've been using your tool for quite some time to visualize mutation locations.

However, I now receive an error when using the tool.

./lollipops -U P26640 -o test.png R273C R175H T125 R248Q -f=/share/YC_Dir/chengxc/software/lollipops/lollipops-v1.5.4-linux64/Arial.ttf
shows

no font loaded - cannot make PNG!

if I use this： lollipops-v1.5.4-linux64/lollipops -U P26640 -o test.png R273C R175H T125 R248Q ERROR: Unable to find Arial.ttf - Which is required for accurate font sizing. Please use -f=/path/to/arial.ttf or the TrueType (.ttf) font of your choice. Gene Symbol: SYVC_HUMAN Drawing diagram to test.png 2022/09/21 17:03:32 no font loaded - cannot make PNG!

Any idea how to fix this?