+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package lightning
import (
+ _ "embed"
"flag"
"fmt"
"io"
_ "net/http/pprof"
+ "os/exec"
+ "strings"
"git.arvados.org/arvados.git/sdk/go/arvados"
)
type pythonPlot struct{}
+//go:embed plot.py
+var plotscript string
+
func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
var err error
defer func() {
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")
+ outputFilename := flags.String("o", "", "output `filename` (e.g., './plot.png')")
+ sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
+ phenotypeFilename := flags.String("phenotype", "", "use `phenotype.csv` as id->phenotype mapping (column 0 is sample id)")
+ cat1Column := flags.Int("phenotype-cat1-column", 1, "0-based column `index` of 1st category in phenotype.csv file")
+ cat2Column := flags.Int("phenotype-cat2-column", -1, "0-based column `index` of 2nd category in phenotype.csv file")
+ xComponent := flags.Int("x", 1, "1-based PCA component to plot on x axis")
+ yComponent := flags.Int("y", 2, "1-based PCA component to plot on y axis")
priority := flags.Int("priority", 500, "container request priority")
+ runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
return 0
} else if err != nil {
return 2
+ } else if flags.NArg() > 0 {
+ err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
+ return 2
}
runner := arvadosContainerRunner{
},
},
}
- err = runner.TranslatePaths(inputFilename, sampleCSVFilename, sampleFastaDirname)
- if err != nil {
- return 1
+ if !*runlocal {
+ err = runner.TranslatePaths(inputFilename, sampleListFilename, phenotypeFilename)
+ if err != nil {
+ return 1
+ }
+ *outputFilename = "/mnt/output/plot.png"
+ }
+ args = []string{
+ *inputFilename,
+ fmt.Sprintf("%d", *xComponent),
+ fmt.Sprintf("%d", *yComponent),
+ *sampleListFilename,
+ *phenotypeFilename,
+ fmt.Sprintf("%d", *cat1Column),
+ fmt.Sprintf("%d", *cat2Column),
+ *outputFilename,
+ }
+ if *runlocal {
+ if *outputFilename == "" {
+ fmt.Fprintln(stderr, "error: must specify -o filename.png in local mode (or try -help)")
+ return 1
+ }
+ cmd := exec.Command("python3", append([]string{"-"}, args...)...)
+ cmd.Stdin = strings.NewReader(plotscript)
+ cmd.Stdout = stdout
+ cmd.Stderr = stderr
+ err = cmd.Run()
+ if err != nil {
+ return 1
+ }
+ return 0
}
runner.Prog = "python3"
- runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"}
+ runner.Args = append([]string{"/plot.py"}, args...)
var output string
output, err = runner.Run()
if err != nil {
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)
-`
projects / lightning.git / blobdiff