root/galaxy-central/tools/filters/bed2gff.xml

リビジョン 2, 4.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
20This tool converts data from BED format to GFF format (scroll down for format description).
21
22--------
23
24**Example**
25
26The 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
30Will 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
55The 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
61The 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。