| Previous changeset 0:7f39014f9404 (2015-03-20) |
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Commit message:
Uploaded |
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modified:
find_subsequences.py find_subsequences.xml tool_dependencies.xml |
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added:
test-data/find_subsequences_advanced_result2.bed test-data/find_subsequences_advanced_result3.bed |
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| diff -r 7f39014f9404 -r d882a0a75759 find_subsequences.py --- a/find_subsequences.py Fri Mar 20 06:23:17 2015 -0400 +++ b/find_subsequences.py Fri Apr 10 06:49:30 2015 -0400 |
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| @@ -10,7 +10,7 @@ choices = ['embl', 'fasta', 'fastq-sanger', 'fastq', 'fastq-solexa', 'fastq-illumina', 'genbank', 'gb'] -def find_pattern(seqs, pattern, outfile_path): +def find_pattern(seqs, pattern, outfile_path, strand): """ Finds all occurrences of a pattern in the a given sequence. Outputs sequence ID, start and end postion of the pattern. @@ -23,8 +23,10 @@ with open(outfile_path, 'w+') as outfile: for seq in seqs: - search_func(seq, pattern, outfile) - search_func(seq, rev_compl, outfile, '-') + if strand in ['both', 'forward']: + search_func(seq, pattern, outfile) + if strand in ['both', 'reverse']: + search_func(seq, rev_compl, outfile, '-') def simple_pattern_search(sequence, pattern, outfile, strand='+'): @@ -50,12 +52,13 @@ if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('-i', '--input' , required=True) - parser.add_argument('-o', '--output' , required=True) - parser.add_argument('-p', '--pattern' , required=True) + parser.add_argument('-i', '--input', required=True) + parser.add_argument('-o', '--output', required=True) + parser.add_argument('-p', '--pattern', required=True) + parser.add_argument('--strand', choices=['both', 'forward', 'reverse'], default='both') parser.add_argument('-f', '--format', default="fasta", choices=choices) args = parser.parse_args() with open(args.input) as handle: - find_pattern( SeqIO.parse(handle, args.format), args.pattern, args.output ) + find_pattern( SeqIO.parse(handle, args.format), args.pattern, args.output, args.strand ) |
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| diff -r 7f39014f9404 -r d882a0a75759 find_subsequences.xml --- a/find_subsequences.xml Fri Mar 20 06:23:17 2015 -0400 +++ b/find_subsequences.xml Fri Apr 10 06:49:30 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.1"> +<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.2"> <description>providing regions in BED format</description> <requirements> <requirement type="package" version="1.65">biopython</requirement> @@ -6,14 +6,15 @@ <command interpreter="python"> <![CDATA[ find_subsequences.py - --input $input - --output $output + --input "${input}" + --output "${output}" --pattern "$pattern_conditional.pattern" #if $input.ext == 'fasta': --format 'fasta' #else: --format 'fastq' #end if + --strand '$strand' ]]> </command> <inputs> @@ -248,6 +249,11 @@ </param> </when> </conditional> + <param name="strand" type="select" label="Search pattern on"> + <option value='both'>both strands</option> + <option value='forward'>forward strand</option> + <option value='reverse'>reverse strand</option> + </param> </inputs> <outputs> <data format="bed" name="output" /> @@ -271,6 +277,20 @@ <param name="pattern_conditional_select" value="user"/> <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/> </test> + <test> + <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> + <param name="pattern" value="atnncg"/> + <param name="strand" value="reverse"/> + <param name="pattern_conditional_select" value="user"/> + <output name="output" file="find_subsequences_advanced_result2.bed" ftype="bed"/> + </test> + <test> + <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> + <param name="pattern" value="atnncg"/> + <param name="strand" value="forward"/> + <param name="pattern_conditional_select" value="user"/> + <output name="output" file="find_subsequences_advanced_result3.bed" ftype="bed"/> + </test> </tests> <help> <![CDATA[ |
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| diff -r 7f39014f9404 -r d882a0a75759 test-data/find_subsequences_advanced_result2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_subsequences_advanced_result2.bed Fri Apr 10 06:49:30 2015 -0400 |
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| @@ -0,0 +1,1 @@ +reverse_advanced 9 15 reverse_advanced - |
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| diff -r 7f39014f9404 -r d882a0a75759 test-data/find_subsequences_advanced_result3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find_subsequences_advanced_result3.bed Fri Apr 10 06:49:30 2015 -0400 |
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| @@ -0,0 +1,1 @@ +forward_advanced 9 15 forward_advanced + |
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| diff -r 7f39014f9404 -r d882a0a75759 tool_dependencies.xml --- a/tool_dependencies.xml Fri Mar 20 06:23:17 2015 -0400 +++ b/tool_dependencies.xml Fri Apr 10 06:49:30 2015 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.65"> - <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.65"> + <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |