func main() {
flag.Usage = func() {
fmt.Fprintf(os.Stderr, "Usage: %s [options] {-U UNIPROT_ID | GENE_SYMBOL} [PROTEIN CHANGES ...]\n", os.Args[0])
fmt.Fprintln(os.Stderr, `
Where GENE_SYMBOL is the official human HGNC gene symbol. This will use the
BioMart API to lookup the UNIPROT_ID. To skip the lookup or use other species,
specify the UniProt ID with -U (e.g. "-U P04637" for TP53)
Protein changes:
Currently only point mutations are supported, and may be specified as:
<AMINO><CODON><AMINO><#COLOR><@COUNT>
Only CODON is required, and AMINO tags are not parsed.
Synonymous mutations are denoted if the first AMINO tag matches the second
AMINO tag, or if the second tag is not present. Otherwise the non-synonymous
mutation color is used. The COLOR tag will override using the #RRGGBB style
provided. The COUNT tag can be used to scale the lollipop marker size so that
the area is exponentially proportional to the count indicated. Examples:
R273C -- non-synonymous mutation at codon 273
T125@5 -- synonymous mutation at codon 125 with "5x" marker sizing
R248Q#00ff00 -- green lollipop at codon 248
R248Q#00ff00@131 -- green lollipop at codon 248 with "131x" marker sizing
(N.B. color must come before count in tags)
Diagram generation options:
-syn-color="#0000ff" color to use for synonymous mutation markers
-mut-color="#ff0000" color to use for non-synonymous mutation markers
-hide-axis do not draw the amino position x-axis
-hide-disordered do not draw disordered regions on the backbone
-hide-motifs do not draw simple motif regions
-labels draw label text above lollipop markers
-no-patterns use solid fill instead of patterns (SVG only)
Output options:
-o=filename.png set output filename (.png or .svg supported)
-w=700 set diagram pixel width (default = automatic fit)
-dpi=300 set DPI (PNG output only)
`)
}
if !drawing.FontLoaded() {
arialPath = flag.String("f", "", "path to arial.ttf")
}
flag.Parse()
drawing.DefaultSettings.ShowLabels = *showLabels
drawing.DefaultSettings.HideDisordered = *hideDisordered
drawing.DefaultSettings.HideMotifs = *hideMotifs
drawing.DefaultSettings.HideAxis = *hideAxis
drawing.DefaultSettings.SolidFillOnly = *noPatterns
drawing.DefaultSettings.SynonymousColor = *synColor
drawing.DefaultSettings.MutationColor = *mutColor
drawing.DefaultSettings.GraphicWidth = float64(*width)
if arialPath != nil && *arialPath != "" {
err := drawing.LoadFontPath(*arialPath)
if err != nil {
fmt.Fprintln(os.Stderr, err)
}
}
if !drawing.FontLoaded() {
fmt.Fprintln(os.Stderr, "WARNING: unable to find Arial.ttf - for more accurate font sizing add -f=/path/to/arial.ttf")
}
var err error
varStart := 0
acc := ""
geneSymbol := ""
if *uniprot == "" && flag.NArg() > 0 {
geneSymbol = flag.Arg(0)
varStart = 1
fmt.Fprintln(os.Stderr, "HGNC Symbol: ", flag.Arg(0))
acc, err = data.GetProtID(flag.Arg(0))
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
fmt.Fprintln(os.Stderr, "Uniprot/SwissProt Accession: ", acc)
}
if *uniprot != "" {
acc = *uniprot
}
if flag.NArg() == 0 && *uniprot == "" {
flag.Usage()
os.Exit(1)
}
data, err := data.GetPfamGraphicData(acc)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
if geneSymbol == "" {
geneSymbol = data.Metadata.Identifier
fmt.Fprintln(os.Stderr, "Pfam Symbol: ", geneSymbol)
}
if *output == "" {
*output = geneSymbol + ".svg"
}
f, err := os.OpenFile(*output, os.O_CREATE|os.O_RDWR|os.O_TRUNC, 0644)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
defer f.Close()
fmt.Fprintln(os.Stderr, "Drawing diagram to", *output)
if strings.HasSuffix(strings.ToLower(*output), ".png") {
drawing.DrawPNG(f, *dpi, flag.Args()[varStart:], data)
} else {
drawing.DrawSVG(f, flag.Args()[varStart:], data)
}
}
func main() {
flag.Usage = func() {
fmt.Fprintf(os.Stderr, "Usage: %s [options] {-Q UNIPROT_DB IDENTIFER | -U UNIPROT_ID | GENE_SYMBOL} [PROTEIN CHANGES ...]\n", os.Args[0])
fmt.Fprintln(os.Stderr, `
Protein ID input:
GENE_SYMBOL is the official human HGNC gene symbol. This will use the
UniprotKB API to lookup the UNIPROT_ID.
You can provide a UniProt ID directly with -U (e.g. "-U P04637" for TP53)
For more advanced usage, query UniprotKB's database mappings directly using
a supported identifier with -Q DBNAME. Available DBNAMEs can be found here:
http://www.uniprot.org/help/programmatic_access#id_mapping_examples
RefSeq ID e.g. -Q P_REFSEQ_AC NP_001265252.1
Entrez GeneID e.g. -Q P_ENTREZGENEID 4336
Ensembl ID e.g. -Q ENSEMBL_ID ENSG00000168314
Protein changes:
Currently only point mutations are supported, and may be specified as:
<AMINO><CODON><AMINO><#COLOR><@COUNT>
Only CODON is required, and AMINO tags are not parsed.
Synonymous mutations are denoted if the first AMINO tag matches the second
AMINO tag, or if the second tag is not present. Otherwise the non-synonymous
mutation color is used. The COLOR tag will override using the #RRGGBB style
provided. The COUNT tag can be used to scale the lollipop marker size so that
the area is exponentially proportional to the count indicated. Examples:
R273C -- non-synonymous mutation at codon 273
T125@5 -- synonymous mutation at codon 125 with "5x" marker sizing
R248Q#00ff00 -- green lollipop at codon 248
R248Q#00ff00@131 -- green lollipop at codon 248 with "131x" marker sizing
(N.B. color must come before count in tags)
Diagram generation options:
-legend draw a legend for colored regions
-syn-color="#0000ff" color to use for synonymous mutation markers
-mut-color="#ff0000" color to use for non-synonymous mutation markers
-hide-axis do not draw the amino position x-axis
-show-disordered draw disordered regions on the backbone
-show-motifs draw simple motif regions
-labels draw label text above lollipop markers
-no-patterns use solid fill instead of patterns (SVG only)
-domain-labels=fit hot to apply domain labels (default="truncated")
"fit" = only if fits in space available
"off" = do not draw text in the domains
Output options:
-o=filename.png set output filename (.png or .svg supported)
-w=700 set diagram pixel width (default = automatic fit)
-dpi=300 set DPI (PNG output only)
Local file input:
-l=filename.json use local file instead of Pfam API for graphic data
see: http://pfam.xfam.org/help#tabview=tab9
`)
}
flag.Parse()
drawing.DefaultSettings.ShowLegend = *showLegend
drawing.DefaultSettings.ShowLabels = *showLabels
drawing.DefaultSettings.HideDisordered = !*showDisordered
drawing.DefaultSettings.HideMotifs = !*showMotifs
drawing.DefaultSettings.HideAxis = *hideAxis
drawing.DefaultSettings.SolidFillOnly = *noPatterns
drawing.DefaultSettings.DomainLabelStyle = *domainLabels
drawing.DefaultSettings.SynonymousColor = *synColor
drawing.DefaultSettings.MutationColor = *mutColor
drawing.DefaultSettings.GraphicWidth = float64(*width)
if *fontPath == "" {
err := drawing.LoadDefaultFont()
if err != nil {
fmt.Fprintln(os.Stderr, "ERROR: Unable to find Arial.ttf - Which is required for accurate font sizing.")
fmt.Fprintln(os.Stderr, " Please use -f=/path/to/arial.ttf or the TrueType (.ttf) font of your choice.")
// continue in the hopes that SVG rendering will be ok...
//os.Exit(1)
}
} else {
fname := path.Base(*fontPath)
fname = strings.TrimSuffix(fname, path.Ext(fname))
err := drawing.LoadFont(fname, *fontPath)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
}
var err error
varStart := 0
acc := ""
geneSymbol := ""
if *uniprot == "" && flag.NArg() > 0 {
geneSymbol = flag.Arg(0)
varStart = 1
if *queryDB == "GENENAME" {
fmt.Fprintln(os.Stderr, "HGNC Symbol: ", flag.Arg(0))
acc, err = data.GetProtID(flag.Arg(0))
} else {
fmt.Fprintln(os.Stderr, "Searching for ID: ", flag.Arg(0))
acc, err = data.GetProtMapping(*queryDB, flag.Arg(0))
}
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
fmt.Fprintln(os.Stderr, "Uniprot/SwissProt Accession: ", acc)
}
if *uniprot != "" {
acc = *uniprot
}
if flag.NArg() == 0 && *uniprot == "" {
flag.Usage()
if mousetrap.StartedByExplorer() {
fmt.Fprintln(os.Stderr, `!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
This is a command-line utility for pipeline processing, you probably don't want
to double-click it! Open your command prompt with 'cmd.exe' and try again.
Press Enter/Ctrl-C to quit.`)
fmt.Scanln(&acc)
}
os.Exit(1)
}
var d *data.PfamGraphicResponse
if *localPath != "" {
d, err = data.GetLocalPfamGraphicData(*localPath)
} else {
d, err = data.GetPfamGraphicData(acc)
}
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
if geneSymbol == "" {
geneSymbol = d.Metadata.Identifier
fmt.Fprintln(os.Stderr, "Pfam Symbol: ", geneSymbol)
}
if *output == "" {
*output = geneSymbol + ".svg"
}
f, err := os.OpenFile(*output, os.O_CREATE|os.O_RDWR|os.O_TRUNC, 0644)
if err != nil {
fmt.Fprintln(os.Stderr, err)
os.Exit(1)
}
defer f.Close()
fmt.Fprintln(os.Stderr, "Drawing diagram to", *output)
if strings.HasSuffix(strings.ToLower(*output), ".png") {
drawing.DrawPNG(f, *dpi, flag.Args()[varStart:], d)
} else {
drawing.DrawSVG(f, flag.Args()[varStart:], d)
}
}