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author | vipints <vipin@cbio.mskcc.org> |
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date | Fri, 24 Apr 2015 18:04:27 -0400 |
parents | c42c69aa81f8 |
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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>