| Next changeset 1:723b5b38d88a (2015-11-11) |
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Commit message:
Imported from capsule None |
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added:
fastq_to_fasta.py fastq_to_fasta.xml test-data/fastq_to_fasta_python_1.out test-data/fastq_to_fasta_python_2.out test-data/sanger_full_range_as_cssanger.fastqcssanger test-data/sanger_full_range_masked_N.fastqsanger test-data/sanger_full_range_masked_lowercase.fastqsanger test-data/sanger_full_range_original_sanger.fastqsanger tool_dependencies.xml |
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| diff -r 000000000000 -r 3571553aeb20 fastq_to_fasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_to_fasta.py Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,22 @@ +#Dan Blankenberg +import sys +from galaxy_utils.sequence.fastq import fastqReader +from galaxy_utils.sequence.fasta import fastaWriter + +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 = fastaWriter( open( output_filename, 'wb' ) ) + for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): + out.write( fastq_read ) + out.close() + if num_reads is None: + print "No valid FASTQ reads could be processed." + else: + print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 ) + +if __name__ == "__main__": main() |
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| diff -r 000000000000 -r 3571553aeb20 fastq_to_fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_to_fasta.xml Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,43 @@ +<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0"> + <description>converter</description> + <requirements> + <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> + </requirements> + <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> + <inputs> + <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" /> + </inputs> + <outputs> + <data name="output_file" format="fasta" /> + </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_fasta_python_1.out" /> + </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_fasta_python_2.out" /> + </test> + <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" /> + <output name="output_file" file="fastq_to_fasta_python_1.out" /> + </test> + </tests> + <help> +**What it does** + +This tool converts FASTQ sequencing reads to FASTA sequences. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + + </help> +</tool> |
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| diff -r 000000000000 -r 3571553aeb20 test-data/fastq_to_fasta_python_1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta_python_1.out Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,4 @@ +>FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC +>FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA |
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| diff -r 000000000000 -r 3571553aeb20 test-data/fastq_to_fasta_python_2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta_python_2.out Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,4 @@ +>FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +G2131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 +>FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +G3131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 |
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| diff -r 000000000000 -r 3571553aeb20 test-data/sanger_full_range_as_cssanger.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_cssanger.fastqcssanger Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,8 @@ +@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`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! |
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| diff -r 000000000000 -r 3571553aeb20 test-data/sanger_full_range_masked_N.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_masked_N.fastqsanger Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +NNNNNNNNNNNNNNNNNNNNNCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCNNNNNNNNNNNNNNNNNNNNN ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! |
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| diff -r 000000000000 -r 3571553aeb20 test-data/sanger_full_range_masked_lowercase.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_masked_lowercase.fastqsanger Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +acgtacgtacgtacgtacgtaCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCatgcatgcatgcatgcatgca ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! |
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| diff -r 000000000000 -r 3571553aeb20 test-data/sanger_full_range_original_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_original_sanger.fastqsanger Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! |
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| diff -r 000000000000 -r 3571553aeb20 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:27:22 2014 -0500 |
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| @@ -0,0 +1,6 @@ +<?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" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |