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GFF3 plugin for BioRuby - allows parsing big data GFF3
Ruby Perl
Tag: v0.8.5

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README.rdoc

bio-gff3

GFF3 parser, aimed at parsing big data GFF3 to return sequences of any type, including assembled mRNA, protein and CDS sequences.

Features:

# Take GFF3 (genome browser) information of any type, and assemble sequences, e.g. mRNA and CDS # Options for low memory use and caching of records # Support for external FASTA input files # Use of multi-cores (NYI)

Currently the output is a FASTA file.

You can use this plugin in two ways. First as a standalone program, next as a plugin library to BioRuby.

Install and run gff3-fetch

After installing ruby 1.9, or later, you can use rubygems

gem install bio-gff3

Then, fetch mRNA and CDS information from GFF3 files and output to FASTA:

gff3-fetch mrna test/data/gff/test.gff3
gff3-fetch cds test/data/gff/test.gff3

Development

To use the library

require 'bio-gff3'

For coding examples see ./bin/gff3-fetch and the ./spec/*rb

You can run RSpecs with something like

rspec -I ../bioruby/lib/ spec/*.rb

(supposing you are referring a bioruby source repository)

This implementation depends on BioRuby's basic GFF3 parser, with the possible advantage that the plugin can assemble sequences, is faster and does not consume all memory. The Gff3 specs are based on the output of the Wormbase genome browser.

See also

gff3-fetch --help

For a write-up see thebird.nl/bioruby/BioRuby_GFF3.html


Copyright

Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>

Fetch and assemble GFF3 types (e.g. ORF, mRNA, CDS) + print in FASTA format. 

  gff3-fetch [--low-mem] [--validate] type [filename.fa] filename.gff3

Where (NYI == Not Yet Implemented):

  --translate     : output as amino acid sequence 
  --validate      : validate GFF3 file by translating
  --fix           : check 3-frame translation and fix, if possible 
  --fix-wormbase  : fix 3-frame translation on ORFs named 'gene1'
  --no-assemble   : output each record as a sequence -- NYI
  --add-phase     : output records using phase (useful w. no-assemble CDS to AA) --NYI

type is any valid type in the GFF3 definition. For example:

  mRNA            : assemble mRNA
  CDS             : assemble CDS 
  exon            : list all exons
  gene|ORF        : list gene ORFs 
  other           : use any type from GFF3 definition, e.g. 'Terminate' -- NYI

and the following performance options:

  --cache full    : load all in RAM (fast)
  --cache none    : do not load anything in memory (slow)
  --low-mem       : use LRU cache (limit RAM use, fast) -- NYI
  --max-cpus num  : use num threads -- NYI
  --emboss        : use EMBOSS translation (fast) -- NYI

Multiple GFF3 files can be used. With external FASTA files, always the last
one before the GFF3 filename is matched.

Note that above switches are only partially implemented at this stage. Full
feature support is projected Feb. 2011.

Examples:

  Assemble mRNA and CDS information from test.gff3 (which includes sequence information)

    gff3-fetch mRNA test/data/gff/test.gff3
    gff3-fetch CDS test/data/gff/test.gff3

  Find CDS records from external FASTA file, adding phase and translate to protein sequence

    gff3-fetch --no-assemble --add-phase --translate CDS test/data/gff/MhA1_Contig1133.fa test/data/gff/MhA1_Contig1133.gff3

  Find mRNA from external FASTA file, without loading everything in RAM

    gff3-fetch --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
    gff3-fetch --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   

  Validate GFF3 file using EMBOSS translation and validation

    gff3-fetch --cache none --validate --emboss mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   

  Find GENEID predicted terminal exons

    gff3-fetch terminal chromosome1.fa geneid.gff3

Performance

time gff3-fetch cds m_hapla.WS217.dna.fa m_hapla.WS217.gff3 > test.fa

Cache      real     user     sys
----------------------------------------------------
full       12m41s   12m28s   0m09s (0.8.0 Jan. 2011)
none      504m39s  477m49s  26m50s (0.8.0 Jan. 2011)
----------------------------------------------------

where

 52M m_hapla.WS217.dna.fa
456M m_hapla.WS217.gff3

ruby 1.9.2p136 (2010-12-25 revision 30365) [x86_64-linux] on an 8 CPU, 2.6 GHz (6MB cache), 16 GB RAM machine.

Cite

If you use this software, please cite 

  http://dx.doi.org/10.1093/bioinformatics/btq475

Copyright

Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>

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