[2] | 1 | <tool id="bed2gff1" name="BED-to-GFF" version="2.0.0"> |
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| 2 | <description>converter</description> |
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| 3 | <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command> |
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| 4 | <inputs> |
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| 5 | <param format="bed" name="input" type="data" label="Convert this query"/> |
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| 6 | </inputs> |
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| 7 | <outputs> |
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| 8 | <data format="gff" name="out_file1" /> |
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| 9 | </outputs> |
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| 10 | <tests> |
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| 11 | <test> |
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| 12 | <param name="input" value="9.bed"/> |
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| 13 | <output name="out_file1" file="bed2gff_out.gff"/> |
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| 14 | </test> |
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| 15 | </tests> |
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| 16 | <help> |
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| 17 | |
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| 18 | **What it does** |
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| 19 | |
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| 20 | This tool converts data from BED format to GFF format (scroll down for format description). |
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| 21 | |
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| 22 | -------- |
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| 23 | |
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| 24 | **Example** |
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| 25 | |
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| 26 | The following data in BED format:: |
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| 27 | |
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| 28 | chr28 346187 388197 BC114771 0 + 346187 388197 0 9 144,81,115,63,155,96,134,105,112, 0,24095,26190,31006,32131,33534,36994,41793,41898, |
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| 29 | |
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| 30 | Will be converted to GFF (**note** that the start coordinate is incremented by 1):: |
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| 31 | |
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| 32 | ##gff-version 2 |
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| 33 | ##bed_to_gff_converter.py |
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| 34 | |
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| 35 | chr28 bed2gff mRNA 346188 388197 0 + . mRNA BC114771; |
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| 36 | chr28 bed2gff exon 346188 346331 0 + . exon BC114771; |
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| 37 | chr28 bed2gff exon 370283 370363 0 + . exon BC114771; |
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| 38 | chr28 bed2gff exon 372378 372492 0 + . exon BC114771; |
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| 39 | chr28 bed2gff exon 377194 377256 0 + . exon BC114771; |
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| 40 | chr28 bed2gff exon 378319 378473 0 + . exon BC114771; |
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| 41 | chr28 bed2gff exon 379722 379817 0 + . exon BC114771; |
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| 42 | chr28 bed2gff exon 383182 383315 0 + . exon BC114771; |
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| 43 | chr28 bed2gff exon 387981 388085 0 + . exon BC114771; |
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| 44 | chr28 bed2gff exon 388086 388197 0 + . exon BC114771; |
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| 45 | |
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| 46 | |
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| 47 | ------ |
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| 48 | |
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| 49 | .. class:: informark |
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| 50 | |
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| 51 | **About formats** |
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| 52 | |
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| 53 | **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: |
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| 54 | |
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| 55 | The first three BED fields (required) are:: |
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| 56 | |
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| 57 | 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). |
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| 58 | 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) |
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| 59 | 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). |
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| 60 | |
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| 61 | The additional BED fields (optional) are:: |
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| 62 | |
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| 63 | 4. name - The name of the BED line. |
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| 64 | 5. score - A score between 0 and 1000. |
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| 65 | 6. strand - Defines the strand - either '+' or '-'. |
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| 66 | 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. |
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| 67 | 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. |
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| 68 | 9. reserved - This should always be set to zero. |
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| 69 | 10. blockCount - The number of blocks (exons) in the BED line. |
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| 70 | 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. |
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| 71 | 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. |
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| 72 | 13. expCount - The number of experiments. |
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| 73 | 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. |
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| 74 | 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. |
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| 75 | |
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| 76 | **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:: |
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| 77 | |
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| 78 | 1. seqname - Must be a chromosome or scaffold. |
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| 79 | 2. source - The program that generated this feature. |
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| 80 | 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". |
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| 81 | 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
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| 82 | 5. end - The ending position of the feature (inclusive). |
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| 83 | 6. score - A score between 0 and 1000. If there is no score value, enter ".". |
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| 84 | 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). |
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| 85 | 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 '.'. |
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| 86 | 9. group - All lines with the same group are linked together into a single item. |
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| 87 | |
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| 88 | </help> |
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| 89 | </tool> |
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