changeset 8:534516105ca9

visualize.py: The second tool, for a more aesthetic, abstract visualization.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize.py	Sun Mar 02 23:47:41 2014 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/python
+import sys
+import random
+import hashlib
+import Image
+import ImageDraw
+
+def main():
+
+  if len(sys.argv) == 1:
+    print """USAGE:
+  $ ./visualize.py genome.fa outfile.png pxsize
+The last two arguments are optional, but must be in those positions.
+If no outfile name is given, it will attempt to display the image directly.
+If no pxsize is given, the default is 512. A power of 2 is highly
+recommended as the resulting image will be much better laid out."""
+    sys.exit(0)
+
+  DEFAULT_SIZE = (512,512)
+  size = DEFAULT_SIZE
+  if len(sys.argv) > 3:
+    user_size = int(sys.argv[3])
+    size = (user_size,user_size)
+
+  # can skip hashing and specify the seed as an option (for testing)
+  if len(sys.argv) > 4:
+    seed = sys.argv[4]
+  else:
+    seed = get_hash(sys.argv[1])
+  print "seed: "+seed
+  random.seed(seed)
+  level = 1
+  layers = []
+  image = draw_layer(size, level)
+  while 1:
+    level+=1
+    layers.append(draw_layer(size, level))
+    if layers[-1] == False:
+      break
+    # opacity = 256/2**level                        # opacity #1
+    opacity = 256/2**(level-1)                    # opacity #2
+    # opacity = 256*(level/2)/2**(level-1)          # opacity #3
+    # opacity = 256*(level/float(2**level))         # opacity #4
+    print "opacity: "+str(int(opacity/2.56))+"%"
+    mask = Image.new("L", size, color=opacity)
+    image.paste(layers[-1], (0,0), mask)
+
+  if len(sys.argv) > 2:
+    image.save(sys.argv[2], 'PNG')
+  else:
+    image.show()
+
+def draw_layer(image_size, level):
+  """Draw every block for a particular layer
+  (blocks of a particular pixel size).
+  Returns an image of the finished layer."""
+  (image_width,image_height) = image_size
+  (width, height) = block_size(image_size, level)
+  if width < 1 or height < 1:
+    return False
+  print "width, height: "+str(width)+", "+str(height)
+  layer = Image.new("RGB", image_size, (0,0,0))
+  draw = ImageDraw.Draw(layer)
+  (x,y) = (0,0)
+  while y < image_height:
+    while x < image_width:
+      draw.rectangle([(x,y), (x+width-1, y+height-1)], fill=randcolor())
+      x += width
+    y += height
+    x = 0
+  return layer
+
+def get_hash(filepath):
+  """Compute hash of the file"""
+  hashed = hashlib.sha256()
+  with open(filepath, 'rb') as filehandle:
+    for chunk in iter(lambda: filehandle.read(65536), b''):
+      hashed.update(chunk)
+  return hashed.hexdigest()
+
+def randcolor():
+  """Return a tuple of random color values"""
+  color = []
+  for i in range(3):
+    color.append(random.randrange(0,255))
+  return tuple(color)
+
+def block_size(image_size, level):
+  """Compute the block width and height for this layer."""
+  (width,height) = image_size
+  while level > 0:
+    width = width/2
+    height = height/4
+    level-=1
+    if level < 1:
+      break
+    width = width/4
+    height = height/2
+    level-=1
+  return (width,height)
+
+def format_genome():
+  """Eventually I'd like to attempt to process the genome file into a standard
+  format, stripping out details of representation that can change the output,
+  such as:
+    - upper/lowercase
+    - line endings
+    - chromosome naming
+    - chromosome order
+    - noncanonical chromosomes"""
+
+def check_genome():
+  """Eventually I'd like this to check assumptions I might make about the
+  genome file. A first check would be that it contains all the chromosomes, in
+  the format ''>chr1' or ''>1'. If these assumptions (which format_genome()
+  depends on) aren't met, and the format isn't recognized, then default to a
+  straight digest of the unmodified file."""
+
+if __name__ == "__main__":
+  main()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize.xml	Sun Mar 02 23:47:41 2014 -0500
@@ -0,0 +1,24 @@
+<tool id="dnagram" name="DNA graphic" version="0.1">
+  <description>Create a graphic from a DNA sequence</description>
+  <command interpreter="python">visualize.py $input $output $size
+  </command>
+  <inputs>
+    <param name="input" type="data" format="fasta,text" label="Input sequence" />
+    <param name="size" type="integer" value="512" min="0" max="16384" label="Output image width (pixels)" help="Height will be the same. A power of 2 is recommended." />
+  </inputs>
+  <outputs>
+    <data name="output" format="png"/>
+  </outputs>
+
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool creates a graphic representing a DNA sequence.  
+The graphic is derived from the sequence, but is not a literal representation. It is intended to be an aesthetic visual based on the sequence. Even a small change in the input sequence will result in a drastically different image. See [here](http://nstoler.com/misc/yourgenome.html) for a full description and rationale.
+
+  </help>
+
+</tool>