returns flanking region/s for every geneget_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
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**Example 1**
- For the following query::
chr22 1000 7000 NM_174568 0 +
- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
chr22 500 800 NM_174568 0 +
.. image:: ../static/operation_icons/flanks_ex1.gif
**Example 2**
- For the following query::
chr22 1000 7000 NM_028946 0 -
- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
chr22 500 800 NM_028946 0 -
.. image:: ../static/operation_icons/flanks_ex2.gif