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comparison tools/filters/bed2gff.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
2 <description>converter</description>
3 <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
4 <inputs>
5 <param format="bed" name="input" type="data" label="Convert this query"/>
6 </inputs>
7 <outputs>
8 <data format="gff" name="out_file1" />
9 </outputs>
10 <tests>
11 <test>
12 <param name="input" value="9.bed"/>
13 <output name="out_file1" file="bed2gff_out.gff"/>
14 </test>
15 </tests>
16 <help>
17
18 **What it does**
19
20 This tool converts data from BED format to GFF format (scroll down for format description).
21
22 --------
23
24 **Example**
25
26 The following data in BED format::
27
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,
29
30 Will be converted to GFF (**note** that the start coordinate is incremented by 1)::
31
32 ##gff-version 2
33 ##bed_to_gff_converter.py
34
35 chr28 bed2gff mRNA 346188 388197 0 + . mRNA BC114771;
36 chr28 bed2gff exon 346188 346331 0 + . exon BC114771;
37 chr28 bed2gff exon 370283 370363 0 + . exon BC114771;
38 chr28 bed2gff exon 372378 372492 0 + . exon BC114771;
39 chr28 bed2gff exon 377194 377256 0 + . exon BC114771;
40 chr28 bed2gff exon 378319 378473 0 + . exon BC114771;
41 chr28 bed2gff exon 379722 379817 0 + . exon BC114771;
42 chr28 bed2gff exon 383182 383315 0 + . exon BC114771;
43 chr28 bed2gff exon 387981 388085 0 + . exon BC114771;
44 chr28 bed2gff exon 388086 388197 0 + . exon BC114771;
45
46
47 ------
48
49 .. class:: informark
50
51 **About formats**
52
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:
54
55 The first three BED fields (required) are::
56
57 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
58 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
59 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
60
61 The additional BED fields (optional) are::
62
63 4. name - The name of the BED line.
64 5. score - A score between 0 and 1000.
65 6. strand - Defines the strand - either '+' or '-'.
66 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
67 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
68 9. reserved - This should always be set to zero.
69 10. blockCount - The number of blocks (exons) in the BED line.
70 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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.
72 13. expCount - The number of experiments.
73 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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.
75
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::
77
78 1. seqname - Must be a chromosome or scaffold.
79 2. source - The program that generated this feature.
80 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
81 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
82 5. end - The ending position of the feature (inclusive).
83 6. score - A score between 0 and 1000. If there is no score value, enter ".".
84 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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 '.'.
86 9. group - All lines with the same group are linked together into a single item.
87
88 </help>
89 </tool>