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gbk_to_gff.xml
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gbk_to_gff.xml
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<tool id="fml_gbk2gff" name="GBK-to-GFF" version="2.1.0">
<description>converter</description>
<requirements>
<requirement type="package" version="1.65">biopython</requirement>
</requirements>
<command interpreter="python">gbk_to_gff.py $inf_gbk > $gff_format
</command>
<inputs>
<param format="gb,gbk,genbank" name="inf_gbk" type="data" label="Convert this query" help="GenBank flat file format consists of an annotation section and a sequence section."/>
</inputs>
<outputs>
<data format="gff" name="gff_format" label="${tool.name} on ${on_string}: Converted"/>
</outputs>
<tests>
<test>
<param name="inf_gbk" value="s_cerevisiae_SCU49845.gbk" />
<output name="gff_format" file="s_cerevisiae_SCU49845.gff" />
</test>
</tests>
<help>
**What it does**
This tool converts data from a GenBank_ flat file format to GFF (scroll down for format description).
.. _GenBank: http://www.ncbi.nlm.nih.gov/genbank/
------
**Example**
- The following data in GenBank format::
LOCUS NM_001202705 2406 bp mRNA linear PLN 28-MAY-2011
DEFINITION Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC)
mRNA, complete cds.
ACCESSION NM_001202705
VERSION NM_001202705.1 GI:334184566.........
FEATURES Location/Qualifiers
source 1..2406
/organism="Arabidopsis thaliana"
/mol_type="mRNA"
/db_xref="taxon:3702"........
gene 1..2406
/gene="THIC"
/locus_tag="AT2G29630"
/gene_synonym="PY; PYRIMIDINE REQUIRING; T27A16.27;........
ORIGIN
1 aagcctttcg ctttaggctg cattgggccg tgacaatatt cagacgattc aggaggttcg
61 ttcctttttt aaaggaccct aatcactctg agtaccactg actcactcag tgtgcgcgat
121 tcatttcaaa aacgagccag cctcttcttc cttcgtctac tagatcagat ccaaagcttc
181 ctcttccagc tatggctgct tcagtacact gtaccttgat gtccgtcgta tgcaacaaca
//
- Will be converted to GFF3::
NM_001202705 gbk2gff chromosome 1 2406 . + 1 ID=NM_001202705;Alias=2;Dbxref=taxon:3702;Name=NM_001202705
NM_001202705 gbk2gff gene 1 2406 . + 1 ID=AT2G29630;Dbxref=GeneID:817513,TAIR:AT2G29630;Name=THIC
NM_001202705 gbk2gff mRNA 192 2126 . + 1 ID=AT2G29630.t01;Parent=AT2G29630
NM_001202705 gbk2gff CDS 192 2126 . + 1 ID=AT2G29630.p01;Parent=AT2G29630.t01
NM_001202705 gbk2gff exon 192 2126 . + 1 Parent=AT2G29630.t01
------
**Reference**
**GBK-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**
**GenBank format** An example of a GenBank record may be viewed here_
.. _here: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
**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::
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**
GBK-to-GFF Wrapper Version 0.6 (Apr 2015)
2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
</help>
</tool>