Mercurial > repos > devteam > dna_filtering

changeset 0:a6f0d355b05f draft

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:55:47 -0400
parents
children 549d2cb4c6f2
files histogram.py histogram2.png histogram2.xml plot_filter.py plotter.py test-data/histogram_in1.tabular test-data/histogram_out1.pdf tool_dependencies.xml
diffstat 8 files changed, 850 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/histogram.py	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+#Greg Von Kuster
+
+import sys
+from rpy import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def main():
+
+    # Handle input params
+    in_fname = sys.argv[1]
+    out_fname = sys.argv[2] 
+    try:
+        column = int( sys.argv[3] ) - 1
+    except:
+        stop_err( "Column not specified, your query does not contain a column of numerical data." )
+    title = sys.argv[4]
+    xlab = sys.argv[5]
+    breaks = int( sys.argv[6] )
+    if breaks == 0:
+        breaks = "Sturges"
+    if sys.argv[7] == "true":
+        density = True
+    else: density = False
+    if len( sys.argv ) >= 9 and sys.argv[8] == "true":
+        frequency = True
+    else: frequency = False
+
+    matrix = []
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_value = ''
+    i = 0
+    for i, line in enumerate( file( in_fname ) ):
+        valid = True
+        line = line.rstrip('\r\n')
+        # Skip comments
+        if line and not line.startswith( '#' ): 
+            # Extract values and convert to floats
+            row = []
+            try:
+                fields = line.split( "\t" )
+                val = fields[column]
+                if val.lower() == "na":
+                    row.append( float( "nan" ) )
+            except:
+                valid = False
+                skipped_lines += 1
+                if not first_invalid_line:
+                    first_invalid_line = i+1
+            else:
+                try:
+                    row.append( float( val ) )
+                except ValueError:
+                    valid = False
+                    skipped_lines += 1
+                    if not first_invalid_line:
+                        first_invalid_line = i+1
+                        invalid_value = fields[column]
+        else:
+            valid = False
+            skipped_lines += 1
+            if not first_invalid_line:
+                first_invalid_line = i+1
+
+        if valid:
+            matrix += row
+
+    if skipped_lines < i:
+        try:
+            a = r.array( matrix )
+            r.pdf( out_fname, 8, 8 )
+            histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
+            if density:
+                density = r.density( a )
+                if frequency:
+                    scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
+                    density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
+                r.lines( density )
+            r.dev_off()
+        except Exception, exc:
+            stop_err( "%s" %str( exc ) )
+    else:
+        if i == 0:
+            stop_err("Input dataset is empty.")
+        else:
+            stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
+
+    print "Histogram of column %s. " %sys.argv[3]
+    if skipped_lines > 0:
+        print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
+
+    r.quit( save="no" )
+    
+if __name__ == "__main__":
+    main()
Binary file histogram2.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/histogram2.xml	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,77 @@
+<tool id="histogram_rpy" name="Histogram" version="1.0.3">
+  <description>of a numeric column</description>
+  <requirements>
+    <requirement type="package" version="1.0.3">rpy</requirement>
+    <requirement type="package" version="2.11.0">R</requirement>
+  </requirements>
+  <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
+    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+    <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
+    <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
+    <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
+    <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
+    <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
+      <param name="numerical_column" value="2"/>
+      <param name="breaks" value="0"/>
+      <param name="title" value="Histogram"/>
+      <param name="xlab" value="V1"/>
+      <param name="density" value="true"/>
+      <param name="frequency" value="false"/>
+      <output name="out_file1" file="histogram_out1.pdf"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
+
+ .. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
+**Syntax**
+
+This tool computes a histogram of the numerical values in a column of a dataset.
+
+- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.
+- **Column for x axis** - only numerical columns are possible.
+- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
+- **Plot title** - the histogram title.
+- **Label for x axis** - the label of the x axis for the histogram.
+- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
+
+-----
+
+**Example**
+
+- Input file::
+
+    1	68	4.1
+    2	71	4.6
+    3	62	3.8
+    4	75	4.4
+    5	58	3.2
+    6	60	3.1
+    7	67	3.8
+    8	68	4.1
+    9	71	4.3
+    10	69	3.7 
+
+- Create a histogram on column 2 of the above dataset. 
+
+.. image:: histogram2.png
+
+</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_filter.py	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,19 @@
+
+def validate(incoming):
+    """Validator for the plotting program"""
+    
+    bins = incoming.get("bins","")
+    col  = incoming.get("col","")
+
+    if not bins or not col:
+        raise Exception, "You need to specify a number for bins and columns"
+
+    try:
+        bins = int(bins)
+        col  = int(col)
+    except:
+        raise Exception, "Parameters are not valid numbers, columns:%s, bins:%s" % (col, bins)
+
+    if not 1<bins<100:
+        raise Exception, "The number of bins %s must be a number between 1 and 100" % bins
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotter.py	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+# python histogram input_file output_file column bins 
+import sys, os
+import matplotlib; matplotlib.use('Agg')
+
+from pylab import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+if __name__ == '__main__':
+    # parse the arguments
+    
+    if len(sys.argv) != 6:
+        stop_err('Usage: python histogram.py input_file column bins output_file style')
+        sys.exit()
+
+    mode = sys.argv[5]
+    HIST = mode == 'hist'
+    try:
+        col =  int(float(sys.argv[2]))
+        if HIST:
+            bin = int(float(sys.argv[3]))
+        else:
+            # hack, this parameter is the plotting style for scatter plots
+            if sys.argv[3] == 'P':
+                style = 'o'
+            elif sys.argv[3] == 'LP':
+                style = 'o-'
+            else:
+                style = '-'
+
+    except:
+        msg = 'Parameter were not numbers %s, %s' % (sys.argv[3], sys.argv[4])
+        stop_err(msg)
+
+    # validate arguments
+    inp_file = sys.argv[1]
+    out_file = sys.argv[4]
+
+    if HIST:
+        print "Histogram on column %s (%s bins)" % (col, bin)
+    else:
+        print "Scatterplot on column %s" % (col)
+
+    xcol= col -1
+    # read the file
+    values = []
+    try:
+        count = 0
+        for line in file(inp_file):
+            count += 1
+            line = line.strip()
+            if line and line[0] != '#':
+                values.append(float(line.split()[xcol]))
+    except Exception, e:
+        stop_err('%s' % e)
+        stop_err("Non numerical data at line %d, column %d" % (count, col) )
+
+    # plot the data
+
+    if HIST:
+        n, bins, patches = hist(values, bins=bin, normed=0)
+    else:
+        plot(values, style)
+    
+    xlabel('values')
+    ylabel('counts')
+
+    if HIST:
+        title('Histogram of values over column %s (%s bins)' % (col, len(bins)) )
+    else:
+        title('Scatterplot over column %s' % col )        
+    grid(True)
+    
+    # the plotter detects types by file extension
+    png_out = out_file + '.png' # force it to png
+    savefig(png_out)
+
+    # shuffle it back and clean up
+    data = file(png_out, 'rb').read() 
+    fp = open(out_file, 'wb')
+    fp.write(data)
+    fp.close()
+    os.remove(png_out)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/histogram_in1.tabular	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,10 @@
+1	68	4.1
+2	71	4.6
+3	62	3.8
+4	75	4.4
+5	58	3.2
+6	60	3.1
+7	67	3.8
+8	68	4.1
+9	71	4.3
+10	69	3.7
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/histogram_out1.pdf	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,545 @@
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+++ b/tool_dependencies.xml	Mon Jul 28 11:55:47 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="rpy" version="1.0.3">
+      <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
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+      <repository changeset_revision="5824d2b3bc8b" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>