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gff_to_gtf.xml
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gff_to_gtf.xml
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<tool id="fml_gff2gtf" name="GFF-to-GTF" version="2.1.0">
<description>converter</description>
<command interpreter="python">gff_to_gtf.py $inf_gff3 > $gtf_format
</command>
<inputs>
<param format="gff3,gff" name="inf_gff3" type="data" label="Convert this query" help="Provide genome annotation file in GFF or GFF3."/>
</inputs>
<outputs>
<data format="gtf" name="gtf_format" label="${tool.name} on ${on_string}: Converted" />
</outputs>
<tests>
<test>
<param name="inf_gff3" value="ens_mm9_chr18.gff3" />
<output name="gtf_format" file="ens_mm9_chr18.gtf" />
</test>
</tests>
<help>
**What it does**
This tool converts data from GFF to GTF file format (scroll down for format description).
--------
**Example**
- The following data in GFF3::
##gff-version 3
17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751
17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
- Will be converted to GTF::
17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
17 protein_coding CDS 7256262 7256957 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352";
17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
--------
**Reference**
**GFF-to-GTF** 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 formats**
**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.
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.
**GTF format** Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields::
1. seqname - The name of the sequence.
2. source - This indicating where the annotation came from.
3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
7. strand - Valid entries include '+', '-', or '.'
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.
9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
--------
**Copyright**
GFF-to-GTF Wrapper Version 0.6 (Apr 2015)
2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center
</help>
</tool>