# HG changeset patch
# User devteam
# Date 1400511613 14400
# Node ID a809505b78afbbcd36f7fb295b47bca879fa098d
Imported from capsule None
diff -r 000000000000 -r a809505b78af short_reads_boxplot.png
Binary file short_reads_boxplot.png has changed
diff -r 000000000000 -r a809505b78af short_reads_figure_score.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/short_reads_figure_score.py Mon May 19 11:00:13 2014 -0400
@@ -0,0 +1,248 @@
+#!/usr/bin/env python
+"""
+boxplot:
+- box: first quartile and third quartile
+- line inside the box: median
+- outlier: 1.5 IQR higher than the third quartile or 1.5 IQR lower than the first quartile
+ IQR = third quartile - first quartile
+- The smallest/largest value that is not an outlier is connected to the box by with a horizontal line.
+"""
+
+import os, sys, math, tempfile, re
+from rpy import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def merge_to_20_datapoints( score ):
+ number_of_points = 20
+ read_length = len( score )
+ step = int( math.floor( ( read_length - 1 ) * 1.0 / number_of_points ) )
+ scores = []
+ point = 1
+ point_sum = 0
+ step_average = 0
+ score_points = 0
+
+ for i in xrange( 1, read_length ):
+ if i < ( point * step ):
+ point_sum += int( score[i] )
+ step_average += 1
+ else:
+ point_avg = point_sum * 1.0 / step_average
+ scores.append( point_avg )
+ point += 1
+ point_sum = 0
+ step_average = 0
+ if step_average > 0:
+ point_avg = point_sum * 1.0 / step_average
+ scores.append( point_avg )
+ if len( scores ) > number_of_points:
+ last_avg = 0
+ for j in xrange( number_of_points - 1, len( scores ) ):
+ last_avg += scores[j]
+ last_avg = last_avg / ( len(scores) - number_of_points + 1 )
+ else:
+ last_avg = scores[-1]
+ score_points = []
+ for k in range( number_of_points - 1 ):
+ score_points.append( scores[k] )
+ score_points.append( last_avg )
+ return score_points
+
+def __main__():
+
+ invalid_lines = 0
+
+ infile_score_name = sys.argv[1].strip()
+ outfile_R_name = sys.argv[2].strip()
+
+ infile_name = infile_score_name
+
+ # Determine tabular or fasta format within the first 100 lines
+ seq_method = None
+ data_type = None
+ for i, line in enumerate( file( infile_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line or line.startswith( '#' ):
+ continue
+ if data_type == None:
+ if line.startswith( '>' ):
+ data_type = 'fasta'
+ continue
+ elif len( line.split( '\t' ) ) > 0:
+ fields = line.split()
+ for score in fields:
+ try:
+ int( score )
+ data_type = 'tabular'
+ seq_method = 'solexa'
+ break
+ except:
+ break
+ elif data_type == 'fasta':
+ fields = line.split()
+ for score in fields:
+ try:
+ int( score )
+ seq_method = '454'
+ break
+ except:
+ break
+ if i == 100:
+ break
+
+ if data_type is None:
+ stop_err( 'This tool can only use fasta data or tabular data.' )
+ if seq_method is None:
+ stop_err( 'Invalid data for fasta format.')
+
+ # Determine fixed length or variable length within the first 100 lines
+ read_length = 0
+ variable_length = False
+ if seq_method == 'solexa':
+ for i, line in enumerate( file( infile_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line or line.startswith( '#' ):
+ continue
+ scores = line.split('\t')
+ if read_length == 0:
+ read_length = len( scores )
+ if read_length != len( scores ):
+ variable_length = True
+ break
+ if i == 100:
+ break
+ elif seq_method == '454':
+ score = ''
+ for i, line in enumerate( file( infile_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line or line.startswith( '#' ):
+ continue
+ if line.startswith( '>' ):
+ if len( score ) > 0:
+ score = score.split()
+ if read_length == 0:
+ read_length = len( score )
+ if read_length != len( score ):
+ variable_length = True
+ break
+ score = ''
+ else:
+ score = score + ' ' + line
+ if i == 100:
+ break
+
+ if variable_length:
+ number_of_points = 20
+ else:
+ number_of_points = read_length
+ read_length_threshold = 100 # minimal read length for 454 file
+ score_points = []
+ score_matrix = []
+ invalid_scores = 0
+
+ if seq_method == 'solexa':
+ for i, line in enumerate( open( infile_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line or line.startswith( '#' ):
+ continue
+ tmp_array = []
+ scores = line.split( '\t' )
+ for bases in scores:
+ nuc_errors = bases.split()
+ try:
+ nuc_errors[0] = int( nuc_errors[0] )
+ nuc_errors[1] = int( nuc_errors[1] )
+ nuc_errors[2] = int( nuc_errors[2] )
+ nuc_errors[3] = int( nuc_errors[3] )
+ big = max( nuc_errors )
+ except:
+ #print 'Invalid numbers in the file. Skipped.'
+ invalid_scores += 1
+ big = 0
+ tmp_array.append( big )
+ score_points.append( tmp_array )
+ elif seq_method == '454':
+ # skip the last fasta sequence
+ score = ''
+ for i, line in enumerate( open( infile_name ) ):
+ line = line.rstrip( '\r\n' )
+ if not line or line.startswith( '#' ):
+ continue
+ if line.startswith( '>' ):
+ if len( score ) > 0:
+ score = ['0'] + score.split()
+ read_length = len( score )
+ tmp_array = []
+ if not variable_length:
+ score.pop(0)
+ score_points.append( score )
+ tmp_array = score
+ elif read_length > read_length_threshold:
+ score_points_tmp = merge_to_20_datapoints( score )
+ score_points.append( score_points_tmp )
+ tmp_array = score_points_tmp
+ score = ''
+ else:
+ score = "%s %s" % ( score, line )
+ if len( score ) > 0:
+ score = ['0'] + score.split()
+ read_length = len( score )
+ if not variable_length:
+ score.pop(0)
+ score_points.append( score )
+ elif read_length > read_length_threshold:
+ score_points_tmp = merge_to_20_datapoints( score )
+ score_points.append( score_points_tmp )
+ tmp_array = score_points_tmp
+
+ # reverse the matrix, for R
+ for i in range( number_of_points - 1 ):
+ tmp_array = []
+ for j in range( len( score_points ) ):
+ try:
+ tmp_array.append( int( score_points[j][i] ) )
+ except:
+ invalid_lines += 1
+ score_matrix.append( tmp_array )
+
+ # generate pdf figures
+ #outfile_R_pdf = outfile_R_name
+ #r.pdf( outfile_R_pdf )
+ outfile_R_png = outfile_R_name
+ r.bitmap( outfile_R_png )
+
+ title = "boxplot of quality scores"
+ empty_score_matrix_columns = 0
+ for i, subset in enumerate( score_matrix ):
+ if not subset:
+ empty_score_matrix_columns += 1
+ score_matrix[i] = [0]
+
+ if not variable_length:
+ r.boxplot( score_matrix, xlab="location in read length", main=title )
+ else:
+ r.boxplot( score_matrix, xlab="position within read (% of total length)", xaxt="n", main=title )
+ x_old_range = []
+ x_new_range = []
+ step = read_length_threshold / number_of_points
+ for i in xrange( 0, read_length_threshold, step ):
+ x_old_range.append( ( i / step ) )
+ x_new_range.append( i )
+ r.axis( 1, x_old_range, x_new_range )
+ r.dev_off()
+
+ if invalid_scores > 0:
+ print 'Skipped %d invalid scores. ' % invalid_scores
+ if invalid_lines > 0:
+ print 'Skipped %d invalid lines. ' % invalid_lines
+ if empty_score_matrix_columns > 0:
+ print '%d missing scores in score_matrix. ' % empty_score_matrix_columns
+
+ r.quit(save = "no")
+
+if __name__=="__main__":__main__()
diff -r 000000000000 -r a809505b78af short_reads_figure_score.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/short_reads_figure_score.xml Mon May 19 11:00:13 2014 -0400
@@ -0,0 +1,87 @@
+
+
+
+ fontconfig
+ rpy
+ R
+
+short_reads_figure_score.py $input1 $output1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: warningmark
+
+To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples).
+
+-----
+
+**What it does**
+
+This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a graph showing score distribution like the one below. Such graph allows you to perform initial evaluation of data quality in a single pass.
+
+-----
+
+**Examples of Quality Data**
+
+Roche (454) or ABI SOLiD data::
+
+ >seq1
+ 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
+
+Illumina (Solexa) data::
+
+ -40 -40 40 -40 -40 -40 -40 40
+
+-----
+
+**Output example**
+
+Quality scores are summarized as boxplot (Roche 454 FLX data):
+
+.. image:: short_reads_boxplot.png
+
+where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines:
+
+ - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths;
+ - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads.
+
+Every box on the plot shows the following values::
+
+ o <---- Outliers
+ o
+ -+- <---- Upper Extreme Value that is no more
+ | than box length away from the box
+ |
+ +--+--+ <---- Upper Quartile
+ | |
+ +-----+ <---- Median
+ | |
+ +--+--+ <---- Lower Quartile
+ |
+ |
+ -+- <---- Lower Extreme Value that is no more
+ than box length away from the box
+ o <---- Outlier
+
+
+
+
+
diff -r 000000000000 -r a809505b78af test-data/454.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/454.qual Mon May 19 11:00:13 2014 -0400
@@ -0,0 +1,52 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
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+27 33 25 34 28 8 26
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+35 24 17 11 5 26 24 40 33 14 34 25 33 24 28 27 27 26 28 28 33 24 36 27 28 27 36 27 27 28 27 28 35 26 27 27 28 27 28 28 28 28 28 27 28 36 27 28 28 28 37 28 27 26 35 26 27 28 28 28
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+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+28 28 26 26 28 26 28 27 28 25 32 22 27 26 25 27 28 28 27 26 27 28 32 23 28 28 34 25 27 22 26 26 27 28 17 28 28 28 28 28 28 34 24 35 25 28 28
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+28 28 28 28 27 43 36 23 11 33 23 27 25 26 28 28 39 33 13 28 27 29 18 28 26 27 26 28 27 28 36 27 26 28 28 28 28 25 28 41 34 17 24 36 28 37 28 28 26 28 17 27 28 26
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
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+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+36 27 25 24 33 23 28 26 28 28 28 28 27 27 26 36 27 36 28 28 28 36 27 28 28 27 27 36 28 28 37 29 28 26 36 27 27 28 27 27 28 27 36 28 28 28 36 27 36 27 28 36 28 25 36 28 28 28 27 28
+39 33 13 28 28 37 28 28 41 34 16 28 28 28 26 36 28 24
diff -r 000000000000 -r a809505b78af test-data/454Score.png
Binary file test-data/454Score.png has changed
diff -r 000000000000 -r a809505b78af test-data/solexa.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/solexa.qual Mon May 19 11:00:13 2014 -0400
@@ -0,0 +1,30 @@
+ -40 -40 40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -15 15 -40 40 -40 -40
+ -40 -40 40 -40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 -5 5 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 21 -40 -21 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 12 -40 -40 -12 -36 -40 36 -40 -40 -40 40 -40 -4 4 -40 -40 -40 -40 -40 40 -40 -40 14 -14 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -25 25
+ -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 34 -40 -34 40 -40 -40 -40 -40 -40 -40 40 -40 -25 25 -40 -40 -40 -40 40 -37 -40 37 -40 -40 7 -40 -7 -40 40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 40 -40 -40 -40 38 -40 -40 -38 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 11 -16 -13 -22 -40 -40 40 -40 -40 -40 -40 40
+ 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -33 33 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 -25 25 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 27 -27 -5 5 -40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 40 -40 -40 -40 -37 37 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -25 25 40 -40 -40 -40 -40 -40 34 -34 -40 40 -40 -40
+ -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -2 2 -40 -40 35 -35 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 40 -40 -40 -40 -40 36 -40 -36 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 5 -5 -40 -28 -40 -16 -40 16 -40 40 -40 -40
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diff -r 000000000000 -r a809505b78af test-data/solexaScore.png
Binary file test-data/solexaScore.png has changed
diff -r 000000000000 -r a809505b78af tool_dependencies.xml
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