|
5
|
1 <tool id="fml_gff2gbk" name="GFF-to-GBK" version="2.0.0">
|
|
|
2 <description>converter</description>
|
|
|
3 <command interpreter="python">gff_to_gbk.py $inf_gff $inf_fas $gbk_format
|
|
|
4 </command>
|
|
|
5 <inputs>
|
|
|
6 <param format="gff,gff3" name="inf_gff" type="data" label="Convert this query" help="Genome annotation in GFF file format."/>
|
|
|
7 <param format="fa,fasta" name="inf_fas" type="data" label="Genome Sequence" help="Genome sequence in FASTA format."/>
|
|
|
8 </inputs>
|
|
|
9 <outputs>
|
|
|
10 <data format="genbank" name="gbk_format" label="${tool.name} on ${on_string}: Converted"/>
|
|
|
11 </outputs>
|
|
|
12 <tests>
|
|
|
13 <test>
|
|
|
14 <param name="inf_gff" value="s_cerevisiae_SCU49845.gff3" />
|
|
|
15 <param name="inf_fas" value="s_cerevisiae_SCU49845.fasta" />
|
|
|
16 <output name="gbk_format" file="s_cerevisiae_SCU49845.gbk" />
|
|
|
17 </test>
|
|
|
18 </tests>
|
|
|
19 <help>
|
|
|
20
|
|
|
21 **What it does**
|
|
|
22
|
|
|
23 This tool converts annotations in GFF to GenBank_ format (scroll down for format description).
|
|
|
24
|
|
|
25 .. _GenBank: http://www.ncbi.nlm.nih.gov/genbank/
|
|
|
26
|
|
|
27 ------
|
|
|
28
|
|
|
29 **Example**
|
|
|
30
|
|
|
31 - The following data in GFF::
|
|
|
32
|
|
|
33 ##gff-version 3
|
|
|
34 # sequence-region NM_001202705 1 2406
|
|
|
35 NM_001202705 GenBank chromosome 1 2406 . + 1 ID=NM_001202705;Alias=2;Dbxref=taxon:3702;Name=NM_001202705;Note=Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC) mRNA%2C complete cds.,REVIEWED REFSEQ;
|
|
|
36 NM_001202705 GenBank gene 1 2406 . + 1 ID=AT2G29630;Dbxref=GeneID:817513,TAIR:AT2G29630;Name=THIC;locus_tag=AT2G29630
|
|
|
37 NM_001202705 GenBank mRNA 192 2126 . + 1 ID=AT2G29630.t01;Parent=AT2G29630
|
|
|
38 NM_001202705 GenBank CDS 192 2126 . + 1 ID=AT2G29630.p01;Parent=AT2G29630.t01;Dbxref=GI:334184567,GeneID:817513,TAIR:AT2G29630;Name=THIC;Note=thiaminC (THIC)%3B CONTAINS InterPro DOMAIN;rotein_id=NP_001189634.1;
|
|
|
39 NM_001202705 GenBank exon 192 2126 . + 1 Parent=AT2G29630.t01
|
|
|
40 ##FASTA
|
|
|
41 >NM_001202705
|
|
|
42 AAGCCTTTCGCTTTAGGCTGCATTGGGCCGTGACAATATTCAGACGATTCAGGAGGTTCG
|
|
|
43 TTCCTTTTTTAAAGGACCCTAATCACTCTGAGTACCACTGACTCACTCAGTGTGCGCGAT
|
|
|
44
|
|
|
45 - Will be converted to GenBank format::
|
|
|
46
|
|
|
47 LOCUS NM_001202705 2406 bp mRNA linear PLN 28-MAY-2011
|
|
|
48 DEFINITION Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC)
|
|
|
49 mRNA, complete cds.
|
|
|
50 ACCESSION NM_001202705
|
|
|
51 VERSION NM_001202705.1 GI:334184566.........
|
|
|
52 FEATURES Location/Qualifiers
|
|
|
53 source 1..2406
|
|
|
54 /organism="Arabidopsis thaliana"
|
|
|
55 /mol_type="mRNA"
|
|
|
56 /db_xref="taxon:3702"........
|
|
|
57 gene 1..2406
|
|
|
58 /gene="THIC"
|
|
|
59 /locus_tag="AT2G29630"
|
|
|
60 /gene_synonym="PY; PYRIMIDINE REQUIRING; T27A16.27;........
|
|
|
61 ORIGIN
|
|
|
62 1 aagcctttcg ctttaggctg cattgggccg tgacaatatt cagacgattc aggaggttcg
|
|
|
63 61 ttcctttttt aaaggaccct aatcactctg agtaccactg actcactcag tgtgcgcgat
|
|
|
64 121 tcatttcaaa aacgagccag cctcttcttc cttcgtctac tagatcagat ccaaagcttc
|
|
|
65 181 ctcttccagc tatggctgct tcagtacact gtaccttgat gtccgtcgta tgcaacaaca
|
|
|
66 //
|
|
|
67
|
|
|
68 ------
|
|
|
69
|
|
|
70 **About formats**
|
|
|
71
|
|
|
72 **GFF** Generic 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::
|
|
|
73
|
|
|
74 1. seqid - Must be a chromosome or scaffold or contig.
|
|
|
75 2. source - The program that generated this feature.
|
|
|
76 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
|
|
|
77 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
|
|
|
78 5. stop - The ending position of the feature (inclusive).
|
|
|
79 6. score - A score between 0 and 1000. If there is no score value, enter ".".
|
|
|
80 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
|
|
|
81 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 '.'.
|
|
|
82 9. attributes - All lines with the same group are linked together into a single item.
|
|
|
83
|
|
|
84 **GenBank format** Consists of an annotation section and a sequence section. Sample record_
|
|
|
85
|
|
|
86 .. _record: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
|
|
|
87
|
|
|
88
|
|
|
89 --------
|
|
|
90
|
|
|
91 **Copyright**
|
|
|
92
|
|
|
93 2010-2014 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
|
|
|
94
|
|
|
95 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)
|
|
|
96
|
|
|
97 </help>
|
|
|
98 </tool>
|
