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comparison gff_fmap.xml @ 5:6e589f267c14

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author devteam
date Tue, 04 Nov 2014 12:15:19 -0500
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1 <tool id="fml_gfffmap" name="GFF-map" version="2.0.0">
2 <description>features</description>
3 <command interpreter="python">
4 gff_fmap.py $gff_input &gt; $idmapping
5 </command>
6 <inputs>
7 <param format="gff3,gff" name="gff_input" type="data" label="Query file" help="Provide genome annotation file in GFF."/>
8 </inputs>
9 <outputs>
10 <data format="txt" name="idmapping" label="${tool.name} on ${on_string}: parent child id map"/>
11 </outputs>
12 <tests>
13 <test>
14 <param name="gff_input" value="Feature_ID_mapping_W.gff3" />
15 <output name="idmapping" file="Feature_ID_mapping_W.txt" />
16 </test>
17 <test>
18 <param name="gff_input" value="Aly_JGI.gff3" />
19 <output name="idmapping" file="Feature_ID_mapping_R.txt" />
20 </test>
21 </tests>
22 <help>
23
24 **What it does**
25
26 GFF-map provides the features (gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a given GFF file.
27
28 --------
29
30 **Example**
31
32 - The features ID mapping in the following data in GFF3::
33
34 ##gff-version 3
35 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
36 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
37 17 protein_coding protein 7256262 7256960 . + 0 ID=ENSP00000328352;Name=ENSP00000328352
38 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
39 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
40 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
41 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
42
43 - Will be displayed as::
44
45 +-----------------------+---------------------------------+
46 | Parent feature type | Associated child feature type(s)|
47 +-----------------------+---------------------------------+
48 | protein_coding gene | protein_coding mRNA |
49 +-----------------------+---------------------------------+
50 | protein_coding protein| protein_coding CDS |
51 +-----------------------+---------------------------------+
52 | protein_coding mRNA | protein_coding CDS |
53 | | protein_coding exon |
54 | | protein_coding five_prime_UTR |
55 | | protein_coding three_prime_UTR |
56 +-----------------------+---------------------------------+
57
58 --------
59
60 **About formats**
61
62 **GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields::
63
64 1. seqid - Must be a chromosome or scaffold.
65 2. source - The program that generated this feature.
66 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
67 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
68 5. stop - The ending position of the feature (inclusive).
69 6. score - A score between 0 and 1000. If there is no score value, enter ".".
70 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
71 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 '.'.
72 9. attributes - All lines with the same group are linked together into a single item.
73
74 --------
75
76 **Copyright**
77
78 2009-2014 Max Planck Society, University of Tübingen &amp; Memorial Sloan Kettering Cancer Center
79
80 Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G. Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics 10.1093/bioinformatics/btt731 (2014)
81
82 </help>
83 </tool>