Mercurial > repos > devteam > fastq_stats
changeset 2:e2cf940128d5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
| author | devteam |
|---|---|
| date | Sat, 30 Sep 2017 13:55:30 -0400 |
| parents | daaf552153fe |
| children | b1cea1b2fcd0 |
| files | fastq_stats.py fastq_stats.xml test-data/fastq_stats_1_out.tabular tool_dependencies.xml |
| diffstat | 4 files changed, 67 insertions(+), 124 deletions(-) [+] |
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--- a/fastq_stats.py Wed Nov 11 12:42:31 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -#Dan Blankenberg -import sys -from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator - -VALID_NUCLEOTIDES = [ 'A', 'C', 'G', 'T', 'N' ] -VALID_COLOR_SPACE = map( str, range( 7 ) ) + [ '.' ] -SUMMARY_STAT_ORDER = ['read_count', 'min_score', 'max_score', 'sum_score', 'mean_score', 'q1', 'med_score', 'q3', 'iqr', 'left_whisker', 'right_whisker' ] - -def main(): - input_filename = sys.argv[1] - output_filename = sys.argv[2] - input_type = sys.argv[3] or 'sanger' - - aggregator = fastqAggregator() - num_reads = None - fastq_read = None - for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): - aggregator.consume_read( fastq_read ) - out = open( output_filename, 'wb' ) - valid_nucleotides = VALID_NUCLEOTIDES - if fastq_read: - if fastq_read.sequence_space == 'base': - 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' ) - else: - 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' ) - valid_nucleotides = VALID_COLOR_SPACE - for i in range( aggregator.get_max_read_length() ): - column_stats = aggregator.get_summary_statistics_for_column( i ) - out.write( '%i\t' % ( i + 1 ) ) - out.write( '%s\t' * len( SUMMARY_STAT_ORDER ) % tuple( [ column_stats[ key ] for key in SUMMARY_STAT_ORDER ] ) ) - out.write( '%s\t' % ','.join( map( str, column_stats['outliers'] ) ) ) - base_counts = aggregator.get_base_counts_for_column( i ) - for nuc in valid_nucleotides: - out.write( "%s\t" % base_counts.get( nuc, 0 ) ) - extra_nucs = sorted( [ nuc for nuc in base_counts.keys() if nuc not in valid_nucleotides ] ) - out.write( "%s\t%s\n" % ( ','.join( extra_nucs ), ','.join( str( base_counts[nuc] ) for nuc in extra_nucs ) ) ) - out.close() - if num_reads is None: - print "No valid fastq reads could be processed." - else: - print "%i fastq reads were processed." % ( num_reads + 1 ) - print "Based upon quality values and sequence characters, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() ) or "None" ) - ascii_range = aggregator.get_ascii_range() - decimal_range = aggregator.get_decimal_range() - 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 - print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] ) - -if __name__ == "__main__": main()
--- a/fastq_stats.xml Wed Nov 11 12:42:31 2015 -0500 +++ b/fastq_stats.xml Sat Sep 30 13:55:30 2017 -0400 @@ -1,25 +1,27 @@ -<tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.0.0"> - <description>by column</description> - <requirements> - <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> - </requirements> - <command interpreter="python">fastq_stats.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> - <inputs> - <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ File"/> - </inputs> - <outputs> - <data name="output_file" format="tabular" /> - </outputs> - <tests> - <test> - <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> - <output name="output_file" file="fastq_stats_1_out.tabular" /> - </test> - </tests> - <help> +<tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.1.1"> + <description>by column</description> + <requirements> + <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> + </requirements> + <command><![CDATA[ +gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}' + ]]></command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger,fastqsanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqcssanger.gz,fastqsanger.bz2,fastqillumina.bz2,fastqsolexa.bz2,fastqcssanger.bz2" label="FASTQ File"/> + </inputs> + <outputs> + <data name="output_file" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> + <output name="output_file" file="fastq_stats_1_out.tabular" /> + </test> + </tests> + <help><![CDATA[ **What is does** -This tool creates summary statistics on a FASTQ file. +This tool creates summary statistics on a FASTQ file. .. class:: infomark @@ -53,24 +55,19 @@ For example:: #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count - 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 - 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 - 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 - 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 - 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 + 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 + 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 + 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 + 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 + 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 ----- .. class:: warningmark Adapter bases in color space reads are excluded from statistics. - ------- - - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btq281</citation> - </citations> - + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations> </tool>
--- a/test-data/fastq_stats_1_out.tabular Wed Nov 11 12:42:31 2015 -0500 +++ b/test-data/fastq_stats_1_out.tabular Sat Sep 30 13:55:30 2017 -0400 @@ -1,37 +1,37 @@ #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count -1 9 23 34 288 32.0 33.0 33.0 33.0 0.0 33 33 23,34 3 1 4 1 0 -2 9 28 33 287 31.8888888889 30.5 33.0 33.0 2.5 28 33 3 3 2 1 0 -3 9 13 34 268 29.7777777778 27.5 33.0 33.5 6.0 27 34 13 5 1 0 3 0 -4 9 17 33 261 29.0 24.5 33.0 33.0 8.5 17 33 1 2 3 3 0 -5 9 22 33 269 29.8888888889 26.0 33.0 33.0 7.0 22 33 3 3 3 0 0 -6 9 22 33 277 30.7777777778 29.0 33.0 33.0 4.0 28 33 22 5 3 0 1 0 -7 9 21 33 258 28.6666666667 23.0 33.0 33.0 10.0 21 33 4 1 3 1 0 -8 9 12 33 263 29.2222222222 26.5 33.0 33.0 6.5 21 33 12 2 1 1 5 0 -9 9 29 33 290 32.2222222222 31.5 33.0 33.0 1.5 30 33 29 3 3 2 1 0 -10 9 23 33 277 30.7777777778 28.0 33.0 33.0 5.0 23 33 1 4 2 2 0 -11 9 12 33 245 27.2222222222 21.0 31.0 33.0 12.0 12 33 5 2 1 1 0 -12 9 13 33 214 23.7777777778 14.0 24.0 33.0 19.0 13 33 2 4 2 1 0 -13 9 5 33 249 27.6666666667 26.5 31.0 33.0 6.5 24 33 5 2 1 1 5 0 -14 9 5 33 233 25.8888888889 19.5 33.0 33.0 13.5 5 33 3 3 2 1 0 -15 9 15 33 251 27.8888888889 22.5 33.0 33.0 10.5 15 33 5 1 1 2 0 -16 9 23 34 269 29.8888888889 23.5 33.0 33.0 9.5 23 34 3 1 2 3 0 -17 9 13 34 266 29.5555555556 27.0 33.0 33.0 6.0 21 34 13 2 3 1 3 0 -18 9 21 34 272 30.2222222222 26.0 33.0 33.0 7.0 21 34 0 5 1 3 0 -19 9 5 34 244 27.1111111111 24.0 30.0 33.0 9.0 21 34 5 4 4 1 0 0 -20 9 11 34 241 26.7777777778 17.0 32.0 33.0 16.0 11 34 3 4 2 0 0 -21 9 13 33 240 26.6666666667 22.5 27.0 33.0 10.5 13 33 1 4 0 4 0 -22 9 5 33 190 21.1111111111 9.0 21.0 33.0 24.0 5 33 1 4 0 3 1 -23 9 5 33 205 22.7777777778 14.0 26.0 33.0 19.0 5 33 4 4 1 0 0 -24 9 5 33 247 27.4444444444 24.5 31.0 33.0 8.5 21 33 5 1 5 1 2 0 -25 9 11 34 241 26.7777777778 18.5 33.0 33.0 14.5 11 34 3 4 0 2 0 -26 9 5 33 212 23.5555555556 11.5 31.0 33.0 21.5 5 33 0 6 0 3 0 -27 9 5 33 227 25.2222222222 20.0 26.0 33.0 13.0 5 33 3 4 1 1 0 -28 9 21 33 255 28.3333333333 22.5 31.0 33.0 10.5 21 33 2 4 3 0 0 -29 9 5 33 228 25.3333333333 19.5 30.0 33.0 13.5 5 33 2 4 1 2 0 -30 9 10 33 213 23.6666666667 13.5 28.0 33.0 19.5 10 33 3 4 2 0 0 -31 9 5 33 236 26.2222222222 21.0 31.0 33.0 12.0 5 33 1 4 1 3 0 -32 9 5 33 210 23.3333333333 11.5 29.0 33.0 21.5 5 33 3 3 0 3 0 -33 9 5 33 183 20.3333333333 8.0 21.0 33.0 25.0 5 33 1 4 2 2 0 -34 9 5 33 150 16.6666666667 6.0 17.0 25.5 19.5 5 33 3 4 1 1 0 -35 9 13 33 217 24.1111111111 19.5 24.0 31.0 11.5 13 33 1 4 1 3 0 -36 9 5 33 195 21.6666666667 11.5 21.0 32.5 21.0 5 33 3 2 1 3 0 +1 9 23 34 288 32.000000 33.000000 33.000000 33.000000 0.000000 33 33 23,34 3 1 4 1 0 +2 9 28 33 287 31.888889 30.500000 33.000000 33.000000 2.500000 28 33 3 3 2 1 0 +3 9 13 34 268 29.777778 27.500000 33.000000 33.500000 6.000000 27 34 13 5 1 0 3 0 +4 9 17 33 261 29.000000 24.500000 33.000000 33.000000 8.500000 17 33 1 2 3 3 0 +5 9 22 33 269 29.888889 26.000000 33.000000 33.000000 7.000000 22 33 3 3 3 0 0 +6 9 22 33 277 30.777778 29.000000 33.000000 33.000000 4.000000 28 33 22 5 3 0 1 0 +7 9 21 33 258 28.666667 23.000000 33.000000 33.000000 10.000000 21 33 4 1 3 1 0 +8 9 12 33 263 29.222222 26.500000 33.000000 33.000000 6.500000 21 33 12 2 1 1 5 0 +9 9 29 33 290 32.222222 31.500000 33.000000 33.000000 1.500000 30 33 29 3 3 2 1 0 +10 9 23 33 277 30.777778 28.000000 33.000000 33.000000 5.000000 23 33 1 4 2 2 0 +11 9 12 33 245 27.222222 21.000000 31.000000 33.000000 12.000000 12 33 5 2 1 1 0 +12 9 13 33 214 23.777778 14.000000 24.000000 33.000000 19.000000 13 33 2 4 2 1 0 +13 9 5 33 249 27.666667 26.500000 31.000000 33.000000 6.500000 24 33 5 2 1 1 5 0 +14 9 5 33 233 25.888889 19.500000 33.000000 33.000000 13.500000 5 33 3 3 2 1 0 +15 9 15 33 251 27.888889 22.500000 33.000000 33.000000 10.500000 15 33 5 1 1 2 0 +16 9 23 34 269 29.888889 23.500000 33.000000 33.000000 9.500000 23 34 3 1 2 3 0 +17 9 13 34 266 29.555556 27.000000 33.000000 33.000000 6.000000 21 34 13 2 3 1 3 0 +18 9 21 34 272 30.222222 26.000000 33.000000 33.000000 7.000000 21 34 0 5 1 3 0 +19 9 5 34 244 27.111111 24.000000 30.000000 33.000000 9.000000 21 34 5 4 4 1 0 0 +20 9 11 34 241 26.777778 17.000000 32.000000 33.000000 16.000000 11 34 3 4 2 0 0 +21 9 13 33 240 26.666667 22.500000 27.000000 33.000000 10.500000 13 33 1 4 0 4 0 +22 9 5 33 190 21.111111 9.000000 21.000000 33.000000 24.000000 5 33 1 4 0 3 1 +23 9 5 33 205 22.777778 14.000000 26.000000 33.000000 19.000000 5 33 4 4 1 0 0 +24 9 5 33 247 27.444444 24.500000 31.000000 33.000000 8.500000 21 33 5 1 5 1 2 0 +25 9 11 34 241 26.777778 18.500000 33.000000 33.000000 14.500000 11 34 3 4 0 2 0 +26 9 5 33 212 23.555556 11.500000 31.000000 33.000000 21.500000 5 33 0 6 0 3 0 +27 9 5 33 227 25.222222 20.000000 26.000000 33.000000 13.000000 5 33 3 4 1 1 0 +28 9 21 33 255 28.333333 22.500000 31.000000 33.000000 10.500000 21 33 2 4 3 0 0 +29 9 5 33 228 25.333333 19.500000 30.000000 33.000000 13.500000 5 33 2 4 1 2 0 +30 9 10 33 213 23.666667 13.500000 28.000000 33.000000 19.500000 10 33 3 4 2 0 0 +31 9 5 33 236 26.222222 21.000000 31.000000 33.000000 12.000000 5 33 1 4 1 3 0 +32 9 5 33 210 23.333333 11.500000 29.000000 33.000000 21.500000 5 33 3 3 0 3 0 +33 9 5 33 183 20.333333 8.000000 21.000000 33.000000 25.000000 5 33 1 4 2 2 0 +34 9 5 33 150 16.666667 6.000000 17.000000 25.500000 19.500000 5 33 3 4 1 1 0 +35 9 13 33 217 24.111111 19.500000 24.000000 31.000000 11.500000 13 33 1 4 1 3 0 +36 9 5 33 195 21.666667 11.500000 21.000000 32.500000 21.000000 5 33 3 2 1 3 0
--- a/tool_dependencies.xml Wed Nov 11 12:42:31 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="galaxy_sequence_utils" version="1.0.0"> - <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>