// Call execute to use the args (os.Args[1:] by default)
// and run through the command tree finding appropriate matches
// for commands and then corresponding flags.
func (c *Command) Execute() (err error) {
// Regardless of what command execute is called on, run on Root only
if c.HasParent() {
return c.Root().Execute()
}
if EnableWindowsMouseTrap && runtime.GOOS == "windows" {
if mousetrap.StartedByExplorer() {
c.Print(MousetrapHelpText)
time.Sleep(5 * time.Second)
os.Exit(1)
}
}
// initialize help as the last point possible to allow for user
// overriding
c.initHelpCmd()
var args []string
if len(c.args) == 0 {
args = os.Args[1:]
} else {
args = c.args
}
cmd, flags, err := c.Find(args)
if err != nil {
// If found parse to a subcommand and then failed, talk about the subcommand
if cmd != nil {
c = cmd
}
if !c.SilenceErrors {
c.Println("Error:", err.Error())
c.Printf("Run '%v --help' for usage.\n", c.CommandPath())
}
return err
}
err = cmd.execute(flags)
if err != nil {
// If root command has SilentUsage flagged,
// all subcommands should respect it
if !cmd.SilenceUsage && !c.SilenceUsage {
c.Println(cmd.UsageString())
}
// If root command has SilentErrors flagged,
// all subcommands should respect it
if !cmd.SilenceErrors && !c.SilenceErrors {
if err == flag.ErrHelp {
cmd.HelpFunc()(cmd, args)
return nil
}
c.Println("Error:", err.Error())
}
return err
}
return
}
func Mousetrap(app *cli.App) {
oldBefore := app.Before
app.Before = func(c *cli.Context) error {
if mousetrap.StartedByExplorer() {
cmd := exec.Command(os.Args[0], os.Args[1:]...)
cmd.Env = append(os.Environ(), "MOUSETRAP=1")
cmd.Stdin = os.Stdin
cmd.Stdout = os.Stdout
cmd.Stderr = os.Stderr
cmd.Run()
cmd = exec.Command("cmd.exe", "/K")
cmd.Env = os.Environ()
cmd.Stdin = os.Stdin
cmd.Stdout = os.Stdout
cmd.Stderr = os.Stderr
err := cmd.Run()
if err != nil {
fmt.Println("Failed to execute sub-process. Error:", err)
os.Exit(1)
}
os.Exit(0)
}
if oldBefore == nil {
return nil
}
return oldBefore(c)
}
}
func preExecHook(c *Command) {
if mousetrap.StartedByExplorer() {
c.Print(MousetrapHelpText)
time.Sleep(5 * time.Second)
os.Exit(1)
}
}
func init() {
if mousetrap.StartedByExplorer() {
fmt.Println("Don't double-click ponydownloader")
fmt.Println("You need to open cmd.exe and run it from the command line!")
time.Sleep(5 * time.Second)
os.Exit(1)
}
}
func init() {
if runtime.GOOS == "windows" {
if mousetrap.StartedByExplorer() {
fmt.Println("Don't double-click ngrok!")
fmt.Println("You need to open cmd.exe and run it from the command line!")
time.Sleep(5 * time.Second)
os.Exit(1)
}
}
}
// Call execute to use the args (os.Args[1:] by default)
// and run through the command tree finding appropriate matches
// for commands and then corresponding flags.
func (c *Command) Execute() (err error) {
// Regardless of what command execute is called on, run on Root only
if c.HasParent() {
return c.Root().Execute()
}
if EnableWindowsMouseTrap && runtime.GOOS == "windows" {
if mousetrap.StartedByExplorer() {
c.Print(MousetrapHelpText)
time.Sleep(5 * time.Second)
os.Exit(1)
}
}
// initialize help as the last point possible to allow for user
// overriding
c.initHelp()
var args []string
if len(c.args) == 0 {
args = os.Args[1:]
} else {
args = c.args
}
if len(args) == 0 {
// Only the executable is called and the root is runnable, run it
if c.Runnable() {
err = c.execute([]string(nil))
} else {
c.Help()
}
} else {
cmd, flags, e := c.Find(args)
if e != nil {
err = e
} else {
err = cmd.execute(flags)
}
}
if err != nil {
if err == flag.ErrHelp {
c.Help()
} else {
c.Println("Error:", err.Error())
c.Printf("Run '%v help' for usage.\n", c.Root().Name())
}
}
return
}
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)
}
}