Adding draw png subcommand

README.md

@@ -1,5 +1,6 @@
 # Goalign
 [![build](https://github.com/evolbioinfo/goalign/actions/workflows/go.yml/badge.svg)](https://github.com/evolbioinfo/goalign/actions) [![Anaconda-Server Badge](https://anaconda.org/bioconda/goalign/badges/installer/conda.svg)](https://anaconda.org/bioconda/goalign) [![Docker hub](https://img.shields.io/docker/cloud/build/evolbioinfo/goalign)](https://hub.docker.com/r/evolbioinfo/goalign/builds/)
+[![DOI:10.1093/nargab/lqab075](https://zenodo.org/badge/DOI/10.1093/nargab/lqab075.svg)](https://doi.org/10.1093/nargab/lqab075)
 
 ![Goalign Logo](images/logo.png)
 
@@ -144,6 +145,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the
 * divide:      Divide an input alignment in several output files (one per alignment)
 * draw:   Draw alignments
   * biojs:     Display an input alignment in an html file using [BioJS](http://msa.biojs.net/)
+  * png: Display an input alignment in a png file, one sequence per line and one pixel per character
 * extract: Extract several sub-alignments, potentially composed of several blocks, from an input alignment, using an coordinate file
 * identical: Tell whether two alignments are identical
 * mask: Replace positions by N (of nucleotides) or X (if amino-acids)

cmd/draw_png.go

@@ -0,0 +1,69 @@
+package cmd
+
+import (
+	"bufio"
+	"fmt"
+	"os"
+	"path/filepath"
+
+	"github.com/evolbioinfo/goalign/align"
+	"github.com/evolbioinfo/goalign/draw"
+	"github.com/evolbioinfo/goalign/io"
+	"github.com/spf13/cobra"
+)
+
+// pngCmd represents the png command
+var pngCmd = &cobra.Command{
+	Use:   "png",
+	Short: "Draw alignments in a png file",
+	Long: `Draw alignments in a png file
+
+One line per sequence, one pixel per character. 
+Color schemes are specific to the alphabet of sequences: 
+	- The nucleotide colors are from bioSyntax (doi.org/10.1186/s12859-018-2315-y).
+	- The amino acid colors are adapted from "Shapely colours" 
+	  (http://acces.ens-lyon.fr/biotic/rastop/help/colour.htm)
+`,
+	RunE: func(cmd *cobra.Command, args []string) (err error) {
+		var l draw.AlignLayout
+		var aligns *align.AlignChannel
+		var f *os.File
+
+		if aligns, err = readalign(infile); err != nil {
+			io.LogError(err)
+			return
+		}
+
+		nalign := 0
+		for al := range aligns.Achan {
+			fname := drawOutput
+			// Add an index to file output name
+			// if there are several alignments to draw
+			if nalign > 0 {
+				ext := filepath.Ext(fname)
+				fname = fmt.Sprintf("%s_%d.%s", fname[0:len(fname)-len(ext)], nalign, ext)
+			}
+			if f, err = openWriteFile(fname); err != nil {
+				io.LogError(err)
+				return
+			}
+			al.CleanNames(nil)
+			w := bufio.NewWriter(f)
+			l = draw.NewPngLayout(w)
+			l.DrawAlign(al)
+			w.Flush()
+			f.Close()
+			nalign++
+		}
+
+		if aligns.Err != nil {
+			err = aligns.Err
+			io.LogError(err)
+		}
+		return
+	},
+}
+
+func init() {
+	drawCmd.AddCommand(pngCmd)
+}

docs/commands/draw.md

@@ -3,7 +3,7 @@
 ## Commands
 
 ### draw
-This command draws alignments with basic functionalities. So far, output format is html, using [BioJS](http://msa.biojs.net/) library. 
+This command draws alignments with basic functionalities. So far, output format is html, using [BioJS](http://msa.biojs.net/) library, and PNG displaying one sequence per line and one pixel per character.
 
 If the input file contains several alignments, it will write several output files.
 
@@ -15,6 +15,7 @@ Usage:
 
 Available Commands:
   biojs       Draw alignments in html file using msaviewer from biojs
+  png         Draw alignments in a png file
 
 Flags:
   -o, --output string   Alignment draw output file (default "stdout")
@@ -42,6 +43,19 @@ Global Flags:
   -p, --phylip          Alignment is in phylip? default fasta
 ```
 
+* png subcommand
+```
+Usage:
+  goalign draw png [flags]
+
+Global Flags:
+  -i, --align string    Alignment input file (default "stdin")
+      --auto-detect     Auto detects input format (overrides -p and -x)
+      --input-strict    Strict phylip input format (only used with -p)
+  -x, --nexus           Alignment is in nexus? default fasta
+  -o, --output string   Alignment draw output file (default "stdout")
+  -p, --phylip          Alignment is in phylip? default fasta
+```
 #### Examples
 
 * Generating a random alignment and displaying it in html
@@ -50,3 +64,10 @@ goalign random -l 10 --seed 10 | goalign draw biojs -o al.html
 ```
 Should give the following alignment:
 ![HTML Display](draw.png)
+
+* Generating a random nucleotide alignment and displaying it in png
+```
+goalign random -l 10 --seed 10 | goalign draw png -o al.png
+```
+Should give the following image:
+![HTML Display](drawPng.png)

docs/index.md

@@ -76,6 +76,7 @@ Command                                                     | Subcommand |
 [divide](commands/divide.md) ([api](api/divide.md))         |            | Divide an input alignment in several output files
 [draw](commands/draw.md) ([api](api/draw.md))               |            | Draws an input alignment
 --                                                          | biojs      | Displays an input alignment in an html file using biojs
+--                                                          | png        | Displays an input alignment in a png file
 [identical](commands/identical.md) ([api](api/identical.md))|            | Tells whether two alignments are identical
 [mask](commands/mask.md) ([api](api/mask.md))               |            | Mask (with N or X) positions of input alignment
 [mutate](commands/mutate.md) ([api](api/mutate.md))         |            | Adds substitutions (~sequencing errors), or gaps, uniformly in an input alignment

draw/png.go

@@ -0,0 +1,66 @@
+package draw
+
+import (
+	"bufio"
+	"image"
+	"image/color"
+	"image/png"
+
+	"github.com/evolbioinfo/goalign/align"
+)
+
+// Colors from bioSyntax (doi.org/10.1186/s12859-018-2315-y)
+var nucleotideColors = map[rune]color.RGBA{
+	'A': {71, 255, 25, 255}, 'C': {255, 70, 65, 255}, 'G': {240, 144, 0, 255}, 'T': {65, 146, 255, 255},
+	'R': {255, 254, 128, 255}, 'Y': {225, 128, 255, 255}, 'S': {255, 155, 128, 255}, 'W': {128, 255, 242, 255},
+	'K': {144, 184, 44, 255}, 'M': {206, 136, 52, 255}, 'B': {248, 193, 192, 255}, 'D': {199, 255, 185, 255},
+	'H': {191, 216, 249, 255}, 'V': {255, 227, 185, 255}, 'N': {230, 230, 230, 255}, '-': {255, 255, 255, 255},
+	'X': {230, 230, 230, 255}, '.': {255, 255, 255, 255},
+}
+
+// Colors adapted from "Shapely" color scheme http://acces.ens-lyon.fr/biotic/rastop/help/colour.htm
+var aminoAcidColors = map[rune]color.RGBA{
+	'A': {140, 255, 140, 255}, 'G': {255, 255, 255, 255}, 'L': {69, 94, 69, 255}, 'S': {255, 112, 66, 255},
+	'V': {255, 140, 255, 255}, 'T': {184, 76, 0, 255}, 'K': {71, 71, 184, 255}, 'D': {160, 0, 66, 255},
+	'I': {0, 76, 0, 255}, 'N': {255, 124, 112, 255}, 'E': {102, 0, 0, 255}, 'P': {82, 82, 82, 255},
+	'R': {0, 0, 124, 255}, 'F': {83, 76, 66, 255}, 'Q': {255, 76, 76, 255}, 'Y': {140, 112, 76, 255},
+	'H': {112, 112, 255, 255}, 'C': {255, 255, 112, 255}, 'M': {184, 160, 66, 255}, 'W': {79, 70, 0, 255},
+	'B': {255, 0, 255, 255}, 'Z': {255, 0, 255, 255}, 'X': {184, 184, 184, 255}, '-': {0, 0, 0, 255},
+	'.': {0, 0, 0, 255},
+}
+
+type pngLayout struct {
+	writer *bufio.Writer
+}
+
+func NewPngLayout(writer *bufio.Writer) AlignLayout {
+	return &pngLayout{writer}
+}
+
+func (layout *pngLayout) DrawAlign(a align.Alignment) (err error) {
+
+	colors := nucleotideColors
+	if a.Alphabet() == align.AMINOACIDS {
+		colors = aminoAcidColors
+	}
+
+	height := a.NbSequences()
+	width := a.Length()
+
+	img := image.NewRGBA(image.Rect(0, 0, width, height))
+
+	for j, seq := range a.Sequences() {
+		for i, char := range seq.Sequence() {
+			c, ok := colors[char]
+			if !ok {
+				// Set unkown character to black
+				c = color.RGBA{0, 0, 0, 0}
+			}
+			img.Set(i, j, c)
+		}
+	}
+
+	png.Encode(layout.writer, img)
+
+	return nil
+}