package lightning import ( "flag" "fmt" "io" _ "net/http/pprof" "git.arvados.org/arvados.git/sdk/go/arvados" ) type pythonPlot struct{} func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int { var err error defer func() { if err != nil { fmt.Fprintf(stderr, "%s\n", err) } }() flags := flag.NewFlagSet("", flag.ContinueOnError) flags.SetOutput(stderr) projectUUID := flags.String("project", "", "project `UUID` for output data") inputFilename := flags.String("i", "-", "input `file`") sampleCSVFilename := flags.String("labels-csv", "", "use first two columns of `labels.csv` as id->color mapping") sampleFastaDirname := flags.String("sample-fasta-dir", "", "`directory` containing fasta input files") priority := flags.Int("priority", 500, "container request priority") err = flags.Parse(args) if err == flag.ErrHelp { err = nil return 0 } else if err != nil { return 2 } runner := arvadosContainerRunner{ Name: "lightning plot", Client: arvados.NewClientFromEnv(), ProjectUUID: *projectUUID, RAM: 4 << 30, VCPUs: 1, Priority: *priority, Mounts: map[string]map[string]interface{}{ "/plot.py": map[string]interface{}{ "kind": "text", "content": plotscript, }, }, } err = runner.TranslatePaths(inputFilename, sampleCSVFilename, sampleFastaDirname) if err != nil { return 1 } runner.Prog = "python3" runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"} var output string output, err = runner.Run() if err != nil { return 1 } fmt.Fprintln(stdout, output+"/plot.png") return 0 } var plotscript = ` import csv import os import scipy import sys infile = sys.argv[1] X = scipy.load(infile) colors = None if sys.argv[2]: labels = {} for fnm in os.listdir(sys.argv[3]): if '.2.fasta' not in fnm: labels[fnm] = '---' if len(labels) != len(X): raise "len(inputdir) != len(inputarray)" with open(sys.argv[2], 'rt') as csvfile: for row in csv.reader(csvfile): ident=row[0] label=row[1] for fnm in labels: if row[0] in fnm: labels[fnm] = row[1] colors = [] labelcolors = { 'PUR': 'firebrick', 'CLM': 'firebrick', 'MXL': 'firebrick', 'PEL': 'firebrick', 'TSI': 'green', 'IBS': 'green', 'CEU': 'green', 'GBR': 'green', 'FIN': 'green', 'LWK': 'coral', 'MSL': 'coral', 'GWD': 'coral', 'YRI': 'coral', 'ESN': 'coral', 'ACB': 'coral', 'ASW': 'coral', 'KHV': 'royalblue', 'CDX': 'royalblue', 'CHS': 'royalblue', 'CHB': 'royalblue', 'JPT': 'royalblue', 'STU': 'blueviolet', 'ITU': 'blueviolet', 'BEB': 'blueviolet', 'GIH': 'blueviolet', 'PJL': 'blueviolet', } for fnm in sorted(labels.keys()): if labels[fnm] in labelcolors: colors.append(labelcolors[labels[fnm]]) else: colors.append('black') from matplotlib.figure import Figure from matplotlib.patches import Polygon from matplotlib.backends.backend_agg import FigureCanvasAgg fig = Figure() ax = fig.add_subplot(111) ax.scatter(X[:,0], X[:,1], c=colors, s=60, marker='o', alpha=0.5) canvas = FigureCanvasAgg(fig) canvas.print_figure(sys.argv[4], dpi=80) `