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/tools/filters/bed2gff.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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 dataset"/>
 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>