9 "git.arvados.org/arvados.git/sdk/go/arvados"
12 type pythonPlot struct{}
14 func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
18 fmt.Fprintf(stderr, "%s\n", err)
21 flags := flag.NewFlagSet("", flag.ContinueOnError)
22 flags.SetOutput(stderr)
23 projectUUID := flags.String("project", "", "project `UUID` for output data")
24 inputFilename := flags.String("i", "-", "input `file`")
25 sampleCSVFilename := flags.String("labels-csv", "", "use first two columns of `labels.csv` as id->color mapping")
26 sampleFastaDirname := flags.String("sample-fasta-dir", "", "`directory` containing fasta input files")
27 err = flags.Parse(args)
28 if err == flag.ErrHelp {
31 } else if err != nil {
35 runner := arvadosContainerRunner{
36 Name: "lightning plot",
37 Client: arvados.NewClientFromEnv(),
38 ProjectUUID: *projectUUID,
41 Mounts: map[string]map[string]interface{}{
42 "/plot.py": map[string]interface{}{
44 "content": plotscript,
48 err = runner.TranslatePaths(inputFilename, sampleCSVFilename, sampleFastaDirname)
52 runner.Prog = "python3"
53 runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"}
68 X = scipy.load(infile)
73 for fnm in os.listdir(sys.argv[3]):
74 if '.2.fasta' not in fnm:
76 if len(labels) != len(X):
77 raise "len(inputdir) != len(inputarray)"
78 with open(sys.argv[2], 'rt') as csvfile:
79 for row in csv.reader(csvfile):
114 for fnm in sorted(labels.keys()):
115 colors.append(labelcolors[labels[fnm]])
117 from matplotlib.figure import Figure
118 from matplotlib.patches import Polygon
119 from matplotlib.backends.backend_agg import FigureCanvasAgg
121 ax = fig.add_subplot(111)
122 ax.scatter(X[:,0], X[:,1], c=colors, s=60, marker='o', alpha=0.5)
123 canvas = FigureCanvasAgg(fig)
124 canvas.print_figure(sys.argv[4], dpi=80)