-
Notifications
You must be signed in to change notification settings - Fork 16
/
bed_to_gff.xml
95 lines (68 loc) · 4.36 KB
/
bed_to_gff.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
<tool id="fml_bed2gff" name="BED-to-GFF" version="2.1.0">
<description>converter</description>
<command interpreter="python">bed_to_gff.py $inf_bed > $gff_format
</command>
<inputs>
<param format="bed" name="inf_bed" type="data" label="Convert this query" help="Provide genome annotation in 12 column BED format."/>
</inputs>
<outputs>
<data format="gff" name="gff_format" label="${tool.name} on ${on_string}: Converted" />
</outputs>
<tests>
<test>
<param name="inf_bed" value="CCDS30770.bed" />
<output name="gff_format" file="CCDS30770.gff" />
</test>
</tests>
<help>
**What it does**
This tool converts data from a 12 column UCSC wiggle BED format to GFF3 (scroll down for format description).
--------
**Example**
- The following data in UCSC Wiggle BED format::
chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347,
- Will be converted to GFF3::
##gff-version 3
chr1 bed2gff gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3
chr1 bed2gff transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3
chr1 bed2gff exon 11874 12227 0 + . Parent=uc001aaa.3
chr1 bed2gff exon 12613 12721 0 + . Parent=uc001aaa.3
chr1 bed2gff exon 13221 14409 0 + . Parent=uc001aaa.3
--------
**Reference**
**BED-to-GFF** is part of oqtans package and cited as [1]_.
.. [1] Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). `10.1093/bioinformatics/btt731`_
.. _10.1093/bioinformatics/btt731: http://goo.gl/I75poH
--------
**About file 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.
**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. seqid - Must be a chromosome or scaffold or contig.
2. source - The program that generated this feature.
3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. stop - 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. phase - 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. attributes - All lines with the same group are linked together into a single item.
--------
**Copyright**
BED-to-GFF Wrapper Version 0.6 (Apr 2015)
2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
</help>
</tool>