Mercurial > repos > nick > dna_visualizer

changeset 5:58160195728e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Change color setting UI, allow background color setting, limit image size.
author Nick Stoler <nstoler@psu.edu>
date Sun, 02 Mar 2014 22:01:44 -0500
parents 16772d7246e0
children 0c552e103c93
files literal.py literal.xml
diffstat 2 files changed, 39 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- a/literal.py	Sun Mar 02 15:02:00 2014 -0500
+++ b/literal.py	Sun Mar 02 22:01:44 2014 -0500
@@ -6,7 +6,7 @@
 import argparse
 import fastareader
 
-OPT_DEFAULTS = {'size':'512x512', 'verbose':True,
+OPT_DEFAULTS = {'size':'512x512', 'verbose':True, 'background':'255,255,255',
   'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'}
 USAGE = "%(prog)s [options] genome.fasta"
 DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base
@@ -40,8 +40,10 @@
   parser.add_argument('-q', '--quiet', action='store_false', dest='verbose',
     help="""Quiet mode.""")
   group = parser.add_argument_group('Color customization', """Use these options
-    to use custom colors for bases. Specify with a comma-delimited RGB value
-    like "100,150,10".""")
+    to use custom colors for the background and the bases. Specify with a
+    comma-delimited RGB value like "100,150,10".""")
+  group.add_argument('-b', '--background', metavar='R,G,B',
+    help="""default: %(default)s""")
   group.add_argument('-A', metavar='R,G,B',
     help="""default: %(default)s""")
   group.add_argument('-T', metavar='R,G,B',
@@ -54,7 +56,7 @@
   args = parser.parse_args()
 
   try:
-    size = parse_size(args.size)
+    size = parse_int_str(args.size, delim='x', num_ints=2)
   except ValueError:
     parser.print_help()
     fail('\nError: Invalid size string "%s".' % args.size)
@@ -67,13 +69,15 @@
     if os.path.exists(outfile) and not args.clobber:
       fail('Error: Output filename already taken: "%s"' % outfile)
 
+  background = parse_int_str(args.background)
+
   colors = {}
-  colors['A'] = parse_rgb(args.A)
-  colors['T'] = parse_rgb(args.T)
-  colors['G'] = parse_rgb(args.G)
-  colors['C'] = parse_rgb(args.C)
+  colors['A'] = parse_int_str(args.A)
+  colors['T'] = parse_int_str(args.T)
+  colors['G'] = parse_int_str(args.G)
+  colors['C'] = parse_int_str(args.C)
 
-  image = Image.new('RGB', size, 'white')
+  image = Image.new('RGB', size, background)
   pixels = image.load()
 
   done = False
@@ -95,26 +99,16 @@
     image.save(outfile, 'PNG')
 
 
-
-def parse_size(size_str):
-  """Parse size string, return a tuple of (width, height).
-  Accepts size strings in the format "640x480".
+def parse_int_str(string, delim=',', num_ints=3):
+  """Parse string of delimited ints, return them in a tuple.
+  Checks that they are ints, they are delimited by "delim", and there are
+  "num_ints" of them.
   If not valid, raises ValueError."""
-  size = map(int, size_str.split('x'))
-  if len(size) != 2:
+  ints = map(int, string.split(delim))
+  if len(ints) != num_ints:
     raise ValueError
   else:
-    return tuple(size)
-
-
-def parse_rgb(rgb_str):
-  """Parse RGB string, return a tuple of (R, G, B).
-  If not valid, raises ValueError."""
-  rgb = map(int, rgb_str.split(','))
-  if len(rgb) != 3:
-    raise ValueError
-  else:
-    return tuple(rgb)
+    return tuple(ints)
 
 
 def outfile_name(infilename):
--- a/literal.xml	Sun Mar 02 15:02:00 2014 -0500
+++ b/literal.xml	Sun Mar 02 22:01:44 2014 -0500
@@ -2,13 +2,13 @@
   <description>Visualize DNA with colored pixels.</description>
   <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height}
   #if $colors.custom:
-    -A $colors.AR,$colors.AG,$colors.AB -T $colors.TR,$colors.TG,$colors.TB -G $colors.GR,$colors.GG,$colors.GB -C $colors.CR,$colors.CG,$colors.CB 
+    -b $colors.background -G $colors.G -C $colors.C -A $colors.A -T $colors.T 
   #end if
   </command>
   <inputs>
     <param name="input" type="data" format="fasta,text" label="Input sequence" />
-    <param name="width" type="integer" value="512" label="Output image width" help="in pixels" />
-    <param name="height" type="integer" value="512" label="Output image height" help="in pixels" />
+    <param name="width" type="integer" value="512" min="0" max="16384" label="Output image width" help="in pixels (max 16384)" />
+    <param name="height" type="integer" value="512" min="0" max="16384" label="Output image height" help="in pixels (max 16384)" />
     <conditional name="colors">
       <param name="custom" type="select" label="Base colors">
         <option value="" selected="True">Use default colors</option>
@@ -18,29 +18,28 @@
         <!-- do nothing -->
       </when>
       <when value="true">
-        <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' -->
-        <param name="AR" type="integer" value="0" label="A red value" />
-        <param name="AG" type="integer" value="255" label="A green value" />
-        <param name="AB" type="integer" value="0" label="A blue value" />
-        <param name="TR" type="integer" value="255" label="T red value" />
-        <param name="TG" type="integer" value="0" label="T green value" />
-        <param name="TB" type="integer" value="0" label="T blue value" />
-        <param name="GR" type="integer" value="255" label="G red value" />
-        <param name="GG" type="integer" value="255" label="G green value" />
-        <param name="GB" type="integer" value="255" label="G blue value" />
-        <param name="CR" type="integer" value="0" label="C red value" />
-        <param name="CG" type="integer" value="0" label="C green value" />
-        <param name="CB" type="integer" value="255" label="C blue value" />
+        <!-- 'G':'255,255,255', 'C':'0,0,255', 'A':'0,255,0', 'T':'255,0,0' -->
+        <param name="G" type="text" value="255,255,255" label="G RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
+          <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
+        </param>
+        <param name="C" type="text" value="0,0,255" label="C RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
+          <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
+        </param>
+        <param name="A" type="text" value="0,255,0" label="A RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
+          <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
+        </param>
+        <param name="T" type="text" value="255,0,0" label="T RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
+          <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
+        </param>
+        <param name="background" type="text" value="255,255,255" label="background RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)">
+          <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator>
+        </param>
       </when>
     </conditional>
   </inputs>
   <outputs>
     <data name="output" format="png"/>
   </outputs>
-  <stdio>
-    <exit_code range="1:" err_level="fatal"/>
-    <exit_code range=":-1" err_level="fatal"/>
-  </stdio>
 
   <help>