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1 #Dan Blankenberg
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2 import sys
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator
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4
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5 VALID_NUCLEOTIDES = [ 'A', 'C', 'G', 'T', 'N' ]
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6 VALID_COLOR_SPACE = map( str, range( 7 ) ) + [ '.' ]
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7 SUMMARY_STAT_ORDER = ['read_count', 'min_score', 'max_score', 'sum_score', 'mean_score', 'q1', 'med_score', 'q3', 'iqr', 'left_whisker', 'right_whisker' ]
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8
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9 def main():
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10 input_filename = sys.argv[1]
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11 output_filename = sys.argv[2]
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12 input_type = sys.argv[3] or 'sanger'
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13
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14 aggregator = fastqAggregator()
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15 num_reads = None
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16 fastq_read = None
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17 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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18 aggregator.consume_read( fastq_read )
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19 out = open( output_filename, 'wb' )
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20 valid_nucleotides = VALID_NUCLEOTIDES
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21 if fastq_read:
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22 if fastq_read.sequence_space == 'base':
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23 out.write( '#column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW\toutliers\tA_Count\tC_Count\tG_Count\tT_Count\tN_Count\tother_bases\tother_base_count\n' )
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24 else:
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25 out.write( '#column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW\toutliers\t0_Count\t1_Count\t2_Count\t3_Count\t4_Count\t5_Count\t6_Count\t._Count\tother_bases\tother_base_count\n' )
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26 valid_nucleotides = VALID_COLOR_SPACE
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27 for i in range( aggregator.get_max_read_length() ):
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28 column_stats = aggregator.get_summary_statistics_for_column( i )
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29 out.write( '%i\t' % ( i + 1 ) )
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30 out.write( '%s\t' * len( SUMMARY_STAT_ORDER ) % tuple( [ column_stats[ key ] for key in SUMMARY_STAT_ORDER ] ) )
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31 out.write( '%s\t' % ','.join( map( str, column_stats['outliers'] ) ) )
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32 base_counts = aggregator.get_base_counts_for_column( i )
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33 for nuc in valid_nucleotides:
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34 out.write( "%s\t" % base_counts.get( nuc, 0 ) )
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35 extra_nucs = sorted( [ nuc for nuc in base_counts.keys() if nuc not in valid_nucleotides ] )
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36 out.write( "%s\t%s\n" % ( ','.join( extra_nucs ), ','.join( str( base_counts[nuc] ) for nuc in extra_nucs ) ) )
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37 out.close()
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38 if num_reads is None:
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39 print "No valid fastq reads could be processed."
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40 else:
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41 print "%i fastq reads were processed." % ( num_reads + 1 )
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42 print "Based upon quality values and sequence characters, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" )
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43 ascii_range = aggregator.get_ascii_range()
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44 decimal_range = aggregator.get_decimal_range()
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45 print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
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46 print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] )
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47
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48 if __name__ == "__main__": main()
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