19524: plot: get sample list from csv instead of fasta filenames.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/plot.go b/plot.go
index 0367b1241a76291b192723e01dca9f72fd6335b6..1d80e8a21cea9e48174fe6777a2873dc7801ab3b 100644 (file)
--- a/plot.go
+++ b/plot.go
@@ -26,8 +26,8 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
        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")
+       sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
+       colormapFilename := flags.String("colormap", "", "use first two columns of `colormap.csv` as id->color mapping")
        priority := flags.Int("priority", 500, "container request priority")
        err = flags.Parse(args)
        if err == flag.ErrHelp {
@@ -51,12 +51,12 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
                        },
                },
        }
-       err = runner.TranslatePaths(inputFilename, sampleCSVFilename, sampleFastaDirname)
+       err = runner.TranslatePaths(inputFilename, sampleListFilename, colormapFilename)
        if err != nil {
                return 1
        }
        runner.Prog = "python3"
-       runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"}
+       runner.Args = []string{"/plot.py", *inputFilename, *sampleListFilename, *colormapFilename, "/mnt/output/plot.png"}
        var output string
        output, err = runner.Run()
        if err != nil {
@@ -69,6 +69,7 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 var plotscript = `
 import csv
 import os
+import os.path
 import scipy
 import sys
 
@@ -78,13 +79,11 @@ 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):
+    with open(sys.argv[2], 'rt') as samplelist:
+        for row in csv.reader(samplelist):
+            labels[row[1]] = '---'
+    with open(sys.argv[3], 'rt') as colormap:
+        for row in csv.reader(colormap):
             ident=row[0]
             label=row[1]
             for fnm in labels: