details: http://www.bx.psu.edu/hg/galaxy/rev/44f2713a7279 changeset: 3561:44f2713a7279 user: Dan Blankenberg dan@bx.psu.edu date: Wed Mar 24 15:13:57 2010 -0400 description: Add FASTQ <--> Tabular converter tools.
diffstat:
test-data/fastq_to_tabular_out_1.tabular | 2 + test-data/fastq_to_tabular_out_2.tabular | 2 + tool_conf.xml.main | 2 + tool_conf.xml.sample | 2 + tools/fastq/fastq_to_tabular.py | 21 ++++++++++++++++++ tools/fastq/fastq_to_tabular.xml | 30 +++++++++++++++++++++++++ tools/fastq/tabular_to_fastq.py | 29 +++++++++++++++++++++++++ tools/fastq/tabular_to_fastq.xml | 37 ++++++++++++++++++++++++++++++++ 8 files changed, 125 insertions(+), 0 deletions(-)
diffs (169 lines):
diff -r 4c95f1a101f1 -r 44f2713a7279 test-data/fastq_to_tabular_out_1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_tabular_out_1.tabular Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,2 @@ +FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[]^_`abcdefghijklmnopqrstuvwxyz{|}~ +FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ~}|{zyxwvutsrqponmlkjihgfedcba`_^][ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 4c95f1a101f1 -r 44f2713a7279 test-data/fastq_to_tabular_out_2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_tabular_out_2.tabular Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,2 @@ +FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) G2131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[]^_`abcdefghijklmnopqrstuvwxyz{|}~ +FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) G3131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 ~}|{zyxwvutsrqponmlkjihgfedcba`_^][ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 4c95f1a101f1 -r 44f2713a7279 tool_conf.xml.main --- a/tool_conf.xml.main Wed Mar 24 14:14:58 2010 -0400 +++ b/tool_conf.xml.main Wed Mar 24 15:13:57 2010 -0400 @@ -297,6 +297,8 @@ <tool file="fastq/fastq_trimmer.xml" /> <tool file="fastq/fastq_manipulation.xml" /> <tool file="fastq/fastq_to_fasta.xml" /> + <tool file="fastq/fastq_to_tabular.xml" /> + <tool file="fastq/tabular_to_fastq.xml" /> </section> <section name="NGS: Mapping" id="ngs_mapping"> <label text="Illumina" id="illumina"/> diff -r 4c95f1a101f1 -r 44f2713a7279 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed Mar 24 14:14:58 2010 -0400 +++ b/tool_conf.xml.sample Wed Mar 24 15:13:57 2010 -0400 @@ -208,6 +208,8 @@ <tool file="fastq/fastq_trimmer.xml" /> <tool file="fastq/fastq_manipulation.xml" /> <tool file="fastq/fastq_to_fasta.xml" /> + <tool file="fastq/fastq_to_tabular.xml" /> + <tool file="fastq/tabular_to_fastq.xml" /> </section> <section name="NGS: Mapping" id="solexa_tools"> <tool file="sr_mapping/lastz_wrapper.xml" /> diff -r 4c95f1a101f1 -r 44f2713a7279 tools/fastq/fastq_to_tabular.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_to_tabular.py Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,21 @@ +#Dan Blankenberg +import sys +from galaxy_utils.sequence.fastq import fastqReader + +def main(): + input_filename = sys.argv[1] + output_filename = sys.argv[2] + input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary + + num_reads = None + fastq_read = None + out = open( output_filename, 'wb' ) + for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): + out.write( "%s\t%s\t%s\n" % ( fastq_read.identifier[1:].replace( '\t', ' ' ), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) ) + out.close() + if num_reads is None: + print "No valid FASTQ reads could be processed." + else: + print "%i FASTQ reads were converted to Tabular." % ( num_reads + 1 ) + +if __name__ == "__main__": main() diff -r 4c95f1a101f1 -r 44f2713a7279 tools/fastq/fastq_to_tabular.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_to_tabular.xml Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,30 @@ +<tool id="fastq_to_tabular" name="FASTQ to Tabular" version="1.0.0"> + <description>converter</description> + <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" /> + </inputs> + <outputs> + <data name="output_file" format="tabular" /> + </outputs> + <tests> + <!-- basic test --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <output name="output_file" file="fastq_to_tabular_out_1.tabular" /> + </test> + <!-- color space test --> + <test> + <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> + <output name="output_file" file="fastq_to_tabular_out_2.tabular" /> + </test> + </tests> + <help> +**What it does** + +This tool converts FASTQ sequencing reads to a Tabular file. + +Tab characters, if present in the source FASTQ file, will be converted to spaces. + + </help> +</tool> diff -r 4c95f1a101f1 -r 44f2713a7279 tools/fastq/tabular_to_fastq.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/tabular_to_fastq.py Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,29 @@ +#Dan Blankenberg +import sys + +def main(): + input_filename = sys.argv[1] + output_filename = sys.argv[2] + identifier_col = int( sys.argv[3] ) - 1 + sequence_col = int( sys.argv[4] ) - 1 + quality_col = int( sys.argv[5] ) - 1 + + max_col = max( identifier_col, sequence_col, quality_col ) + num_reads = None + fastq_read = None + skipped_lines = 0 + out = open( output_filename, 'wb' ) + for num_reads, line in enumerate( open( input_filename ) ): + fields = line.rstrip( '\n\r' ).split( '\t' ) + if len( fields ) > max_col: + out.write( "@%s\n%s\n+\n%s\n" % ( fields[identifier_col], fields[sequence_col], fields[quality_col] ) ) + else: + skipped_lines += 1 + + out.close() + if num_reads is None: + print "Input was empty." + else: + print "%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % ( num_reads + 1 - skipped_lines ) + +if __name__ == "__main__": main() diff -r 4c95f1a101f1 -r 44f2713a7279 tools/fastq/tabular_to_fastq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/tabular_to_fastq.xml Wed Mar 24 15:13:57 2010 -0400 @@ -0,0 +1,37 @@ +<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0"> + <description>converter</description> + <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Tabular file to convert" /> + <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" /> + <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" /> + <param name="quality" label="Quality column" type="data_column" data_ref="input_file" /> + </inputs> + <outputs> + <data name="output_file" format="fastq" /> + </outputs> + <tests> + <!-- basic test --> + <test> + <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" /> + <param name="identifier" value="1" /> + <param name="sequence" value="2" /> + <param name="quality" value="3" /> + <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> + </test> + <!-- color space test --> + <test> + <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" /> + <param name="identifier" value="1" /> + <param name="sequence" value="2" /> + <param name="quality" value="3" /> + <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> + </test> + </tests> + <help> +**What it does** + +This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. + + </help> +</tool>