converter gff_to_bed_converter.py $input $out_file1

**What it does** This tool converts data from GFF format to BED format (scroll down for format description). -------- **Example** The following data in GFF format:: chr22 GeneA enhancer 10000000 10001000 500 + . TGA chr22 GeneA promoter 10010000 10010100 900 + . TGA Will be converted to BED (**note** that 1 is subtracted from the start coordinate):: chr22 9999999 10001000 enhancer 0 + chr22 10009999 10010100 promoter 0 + ------ .. class:: infomark **About formats** **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several 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 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. **GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:: 1. seqname - Must be a chromosome or scaffold. 2. source - The program that generated this feature. 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". 4. start - The starting position of the feature in the sequence. The first base is numbered 1. 5. end - The ending position of the feature (inclusive). 6. score - A score between 0 and 1000. If there is no score value, enter ".". 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. 9. group - All lines with the same group are linked together into a single item.