expander ucsc_gene_bed_to_intron_bed.py --input=$input1 --output=$out_file1

**Syntax** This tool converts a UCSC gene bed format file to a list of bed format lines corresponding to requested features of each gene. - **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and twelve additional optional ones:: The first three BED fields (required) are: 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). The twelve additional BED fields (optional) are: 4. name - The name of the BED line. 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. 9. reserved - This should always be set to zero. 10. blockCount - The number of blocks (exons) in the BED line. 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. 13. expCount - The number of experiments. 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount. ----- **Example** - A UCSC gene bed format file:: chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126 chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399 - Converts the above file to a list of bed lines, which has the introns:: chr7 127475311 127475993 NM_000230 0 + chr7 127486167 127488406 NM_000230 0 + chr7 127486167 127488409 D49487 0 +