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James Taylor
62 lines
2.3 KiB
XML
62 lines
2.3 KiB
XML
<tool id="Extract genomic DNA 1" name="Extract genomic DNA">
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<description>corresponding to query coordinates</description>
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<command interpreter="perl">fasta-subseq-wrapper.pl -i $input -o $out_file1 -p $input_chromCol $input_startCol $input_endCol $input_strandCol -g $dbkey</command>
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<inputs>
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<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"/>
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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="1.bed"/>
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<output name="out_file1" file="fsa_extract_genomic_dna.dat" />
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</test>
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</tests>
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<help>
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.. class:: warningmark
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Make sure the input data has been specified a database build.
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-----
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**Syntax**
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This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA format.
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- **FASTA format** a text-based format for representing both nucleic and protein sequences, in which base pairs or proteins are represented using a single-letter code.
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- This format contains a one line header. It starts with a " >" symbol. The first word on this line is the name of the sequence. The rest of the line is a description of the sequence.
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- The remaining lines contain the sequence itself.
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- Blank lines in a FASTA file are ignored, and so are spaces or other gap symbols (dashes, underscores, periods) in a sequence.
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- Fasta files containing multiple sequences are just the same, with one sequence listed right after another. This format is accepted for many multiple sequence alignment programs.
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-----
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**Example**
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- Input dataset::
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chr7 127475281 127475310 NM_000230 0 +
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chr7 127485994 127486166 NM_000230 0 +
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chr7 127486011 127486166 D49487 0 +
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- Fetch genomic DNAs of the above data::
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>hg17_chr7_127475281_127475310_+
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GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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>hg17_chr7_127485994_127486166_+
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GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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GATCAATGACATTTCACACACG
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>hg17_chr7_127486011_127486166_+
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TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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ACACG
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</help>
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</tool>
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