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Add additional tests to FASTQ Quality Trimmer tool

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This commit is contained in:
Daniel Blankenberg
2010-04-09 11:35:02 -04:00
parent d93a7fef0f
commit 3d148eaebf
2 changed files with 34 additions and 3 deletions
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tools/fastq/fastq_trimmer_by_quality.py
+8 -3
View File
@@ -55,6 +55,12 @@ def main():
if len ( args ) != 2:
parser.error( "Need to specify an input file and an output file" )
if options.window_size < 1:
parser.error( 'You must specify a strictly positive window size' )
if options.window_step < 1:
parser.error( 'You must specify a strictly positive step size' )
#determine an exhaustive list of window indexes that can be excluded from aggregation
exclude_window_indexes = []
last_exclude_indexes = []
@@ -76,7 +82,6 @@ def main():
out = fastqWriter( open( args[1], 'wb' ), format = options.format )
action = ACTION_METHODS[ options.aggregation_action ]
window_step = abs( options.window_step )
num_reads = None
num_reads_excluded = 0
@@ -93,7 +98,7 @@ def main():
if exclude_and_compare( action, quality_list[ lwindow_position:lwindow_position + options.window_size ], options.score_comparison, options.quality_score, exclude_window_indexes ):
fastq_read = fastq_read.slice( lwindow_position, None )
break
lwindow_position += window_step
lwindow_position += options.window_step
else:
rwindow_position = len( quality_list ) #right position of window
while True:
@@ -105,7 +110,7 @@ def main():
if exclude_and_compare( action, quality_list[ lwindow_position:rwindow_position ], options.score_comparison, options.quality_score, exclude_window_indexes ):
fastq_read = fastq_read.slice( None, rwindow_position )
break
rwindow_position -= window_step
rwindow_position -= options.window_step
if options.keep_zero_length or len( fastq_read ):
out.write( fastq_read )
else:
tools/fastq/fastq_trimmer_by_quality.xml
+26
View File
@@ -94,6 +94,32 @@
<param name="quality_score" value="1"/>
<output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
</test>
<test>
<!-- Trim entire sequences; keep empty reads -->
<param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
<param name="keep_zero_length" value="true" />
<param name="trim_ends" value="53"/>
<param name="window_size" value="1"/>
<param name="step_size" value="1"/>
<param name="exclude_count" value="0"/>
<param name="aggregation_action" value="min"/>
<param name="score_comparison" value="&gt;="/>
<param name="quality_score" value="999"/>
<output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" />
</test>
<test>
<!-- Trim entire sequences; discard empty reads -->
<param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
<param name="keep_zero_length"/>
<param name="trim_ends" value="53"/>
<param name="window_size" value="1"/>
<param name="step_size" value="1"/>
<param name="exclude_count" value="0"/>
<param name="aggregation_action" value="min"/>
<param name="score_comparison" value="&gt;="/>
<param name="quality_score" value="999"/>
<output name="output_file" file="empty_file.dat" />
</test>
</tests>
<help>
This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.