[Bioperl-l] Re: Proposed GFF version 3

Lincoln Stein lstein at cshl.org
Mon Feb 10 13:25:33 EST 2003


Hi Richard,

Do you mean that we should swap columns 9 and 10 entirely, or just swap their 
names?  I think you mean the former, but I want to be sure.

Lincoln

On Monday 10 February 2003 11:12 am, Richard Durbin wrote:
> Hello all,
>
> This looks very nice to me.  Not surprising perhaps because I had an
> earlier involvement as Lincoln says.
>
> I have added gff-list at sanger.ac.uk to the mailing Cc: list because it is
> the "official" GFF mailing list, although it is very little used.
>
> I have one major comment, that columns 9 (group) and 10 (attributes)
> should be switched.  Although GFF version 1 column 9 was called "group"
> in version 2, which is what has been current for over two years, this
> was renamed "attribute" and contains the attribute information.  For
> consistency we should keep column 9 for the attributes.  Also, in many
> cases there will be attributes but no group.
>
> I like ID and Target.  I see the idea with hsp's for gapped alignments,
> though perhaps they could be called "match_block".  But there is a case
> I think to also encode gapped alignments on one line, perhaps using the
> CIGAR encoding used by ENSEMBL (and BioPerl?), e.g. as
>
> 		Target=M1:1..1000;Align=xxxxxxx
>
> (sorry I don't know cigar format well enough to write a legal string.
>
> Richard
>
> Lincoln Stein wrote:
> > This letter is to discuss a proposed extension to GFF.  It arises from
> > conversations with Richard Durbin during last fall's Hinxton genome
> > informatics meeting.
> >
> > Although there are many richer ways of representing genomic features
> > via XML, the stubborn persistence of a variety of ad-hoc tab-delimited
> > flat file formats declares the bioinformatics community's need for a
> > simple format that can be modified with a text editor and processed
> > with shell tools like grep.  The GFF format, although widely used, has
> > fragmented into multiple incompatible dialects.  When asked why they
> > have modified the published Sanger specification, bioinformaticists
> > frequently answer that the format was insufficient for their needs,
> > and they needed to extend it.  The proposed GFF3 format addresses the
> > most common extensions to GFF, while preserving backward compatibility
> > with previous formats. The new format:
> >
> >     1) adds a mechanism for representing more than one level
> >        of hierarchical grouping of features and subfeatures.
> >     2) separates the ideas of group membership and feature name/id
> >     3) constrains the feature type field to be taken from a controlled
> >        vocabulary.
> >     4) allows a single feature, such as an exon, to belong to more than
> >        one group at a time.
> >     5) one level of relative addressing for subfeatures (e.g. exons
> >        can be expressed in transcript coordinates)
> >     6) an explicit convention for pairwise alignments
> >     7) an explicit convention for features that occupy disjunct regions
> >
> > The format consists of 10 columns, separated by spaces.  The following
> > unescaped characters are allowed within fields:
> > [a-zA-Z0-9.:;=%^*$@!+_?-].  All other characters must must be escaped
> > using the URL escaping conventions.  Unescaped quotation marks,
> > backslashes and other ad-hoc escaping conventions that have been added
> > to the GFF format are explicitly forbidden.  The =, ; and % characters
> > have reserved meanings as described below.
> >
> > Undefined fields are replaced with the "." character, as described in
> > the original GFF spec.
> >
> > Column 1: "seqid"
> >
> > The ID of the landmark used to establish the coordinate system for the
> > current feature.  IDs must contain alphanumeric characters.
> > Whitespace, if present, must be escaped using URL escaping rules
> > (e.g. space="%20").
> >
> > Column 2: "source"
> >
> > The source of the feature.  This is unchanged from the older GFF specs
> > and is not part of a controlled vocabulary.
> >
> > Column 3: "type"
> >
> > The type of the feature (previously called the "method").  This is
> > constrained to be either: (a) a term from SOFA; or (b) a SOFA
> > accession number.  The latter alternative is distinguished using the
> > syntax SOFA:000000.
> >
> > Columns 4 & 5: "start" and "end"
> >
> > The start and end of the feature, in 1-based integer coordinates,
> > relative to the landmark given in column 1.  Start is less than end.
> >
> > Column 6: "score"
> >
> > The score of the feature, a floating point number.  As in earlier
> > versions of the format, the semantics of the score are ill-defined.
> > It is strongly recommended that E-values be used for sequence
> > similarity features, and that P-values be used for ab initio gene
> > prediction features.
> >
> > Column 7: "strand"
> >
> > The strand of the feature.  + for positive strand (relative to the
> > landmark), - for minus strand, and . for features that are not
> > stranded.  In addition, ? can be used for features whose strandedness
> > is relevant, but unknown.
> >
> > Column 8: "phase"
> >
> > The phase of the feature, for protein-encoding featues (primarily
> > CDSs).  This is an integer-valued field with the values 0, 1, or 2.
> > The integer indicates the offset from the start of the feature to the
> > first base of the first codon in the reading frame.  "." is used for
> > features that do not corresponding to a reading frame.
> >
> > Column 9: "group"
> >
> > A list of the immediate parents of the current feature.  Multiple
> > parents are allowed (example: one exon shared by multiple
> > transcripts). Multiple parents are separated by a semicolon.
> > Parentless features have a dot in this field.
> >
> > Column 10: "attributes"
> >
> > A list of feature attributes in the format tag=value.  Multiple
> > tag=value pairs are separated by semicolons.  URL escaping rules are
> > used for tags or values containing whitespace, "=" characters and
> > semicolons.
> >
> > Two tags are special:
> >
> >     ID	 Indicates the name of the feature.  IDs must be unique
> > 	 within the scope of the GFF file.
> >
> >     Target Indicates the target of a nucleotide to nucleotide or
> > 	   nucleotide to protein alignment.  The format of the
> > 	   value is "target_id:start..end"  Start may be greater
> > 	   than end to indicate a + strand alignment to the
> > 	   reverse complement of a target nucleotide sequence.
> >
> > In the example GFF3 file given below, the first column contains line
> > numbers that I have added for the purposes of the narrative.  Here are
> > some common scenarios that I have attempted to illustrate:
> >
> > A) a simple feature, no public ID
> >
> > Line 2 in the example is a feature of type "repeat". It has a start
> > and an end and no ID, but it does have an attribute named "Note."
> >
> > B) a simple feature with a public ID
> >
> > Line 3 is a feature of type clone.  It has a start and an end.  Its
> > parent is undefined (empty column 9), but it has an attribute of type
> > ID with value "cTel33B."
> >
> > C) a feature with multiple attributes
> >
> > Line 5 is a feature of type "gene."  It has no parent, and has
> > attributes of type ID, Note, and GO_term.
> >
> > D) a hierarchical grouping of features
> >
> > Lines 5-13 demonstrate a hierarchical grouping.  At the top level is
> > line 5, which defines the extent of a "gene" with ID Y74C9A.1.  Below
> > this are two features of type mRNA (lines 6 and 7).  Their group
> > fields contain the ID of Y74C9A.1, indicating that this feature is
> > their immediate parent.  In the 10th column, the mRNA features have
> > their own IDs independent of the ID of the parent gene.
> >
> > This pattern is repeated for the exons listed on lines 8-11.  Exons
> > e1, e2, and e4 belong to both of the transcripts.  Therefore, both
> > transcript IDs are listed in the group column, separated by
> > semicolons.
> >
> > Exon e3 belongs only to one of the transcripts, and therefore only
> > that transcript's ID is listed in the group column.
> >
> > Lines 12 and 13 indicate coding_start and coding_end features.  These
> > subfeatures are hierarchically grouped underneath their corresponding
> > exons, but they do not have independent public IDs.
> >
> > E) Disjunct coordinates
> >
> > Lines 14-16 illustrates a single feature -- the CDS corresponding to
> > mRNA Y74C9A.1a -- which occupies multiple disjunct regions.  The group
> > column indicates that the CDS belongs to mRNA Y74C9A.1a.  However, the
> > attribute column assigns each of lines 14-16 the same ID.  Because the
> > ID is the same, this is to be interpreted as a single feature that
> > spans multiple locations.
> >
> > F) Alignments
> >
> > Lines 17-19 demonstrate a gapped alignment of two sequences using the
> > reserved Target attribute.  Each non-gapped segment becomes a line in
> > the GFF3 file.  The segments each share the same ID, thereby
> > indicating that the segments are disjunct regions of the same feature.
> > The Target attribute indicates the ID of the target sequence (which
> > does not have to be represented in the GFF3 file) and the start and
> > end coordinates of the aligned target.
> >
> > Unlike the GFF1 and GFF2 formats, the group field for gapped
> > alignments can be empty. However, a valid alternative representation
> > is to create a single "match" feature, and a series of "hsp" features
> > underneath it via the group field.  Lines 20-22 show this alternative
> > representation.
> >
> > G) Relative coordinates
> >
> > Lines 23-26 illustrate using relative coordinate addressing in
> > feature/subfeature relationships.  Line 23 defines an mRNA that is
> > positioned on sequence landmark "I" from positions 5000 to 6000.  Its
> > ID field indicates that it is M7.3.  Lines 24-26 are exon subfeatures
> > of M7.3 as indicated by their group field.  However, the seqid field
> > specifies M7.3 as the parent coordinate system, thereby allowing the
> > exons to begin at position 1.
> >
> >   0  ##gff-version 3
> >   1  ##sequence-region I:1..14972282
> >   2  I       wormbase        repeat  5000    5100    .       .       .   
> >    .       Note=ALU3 3  I       wormbase        clone   1       2679    .
> >       +       .       .       ID=cTel33B 4  I       wormbase       
> > contig  1       14972282        .       +       .       .      
> > ID=CHROMOSOME_I 5  I       wormbase        gene    43733   44677   .     
> >  +       .               .       ID=Y74C9A.1;Note=unc-3;GO_term=GO:12345
> > 6  I       wormbase        mRNA    43733   44677   .       +       .     
> >  Y74C9A.1        ID=Y74C9A.1a 7  I       wormbase        mRNA    43733  
> > 44677   .       +       .       Y74C9A.1        ID=Y74C9A.1b 8  I      
> > wormbase        exon    43733   43961   .       +       .      
> > Y74C9A.1a;Y74C9A.1b     ID=e1 9  I       wormbase        exon    44030  
> > 44234   .       +       .       Y74C9A.1a;T:Y74C9A.1b   ID=e2 10  I      
> > wormbase        exon    44281   44328   .       +       .       Y74C9A.1b
> >       ID=e3 11  I       wormbase        exon    44521   44677   .       +
> >       .       Y74C9A.1a;T:Y74C9A.1b   ID=e4 12  I       wormbase       
> > coding_start    43740   43740   .       +       .       e1 13  I      
> > wormbase        coding_end      44677   44677   .       +       .      
> > e4 14  I       wormbase        cds     43740   43961   .       +       0 
> >      Y74C9A.1a 15  I       wormbase        cds     44030   44234   .     
> >  +       1       Y74C9A.1a 16  I       wormbase        cds     44521  
> > 44677   .       +       1       Y74C9A.1a 17  I       wormbase       
> > match   1       100     100     .       .       .      
> > ID=12345.s;Target=cb123:1001..1100 18  I       wormbase        match  
> > 101     500     20      .       .       .      
> > ID=12345.s;Target=cb123:1101..1500 19  I       wormbase        match  
> > 501     1000    80      .       .       .      
> > ID=12345.s;Target=cb123:1501..2000 20  I       wormbase        match  
> > 5001    6000    100     .       .       .       ID=abc;Target=M1:1..1000
> > 21  I       wormbase        hsp     5001    5500    .       .       .    
> >   abc     Target=M1:1..500 22  I       wormbase        hsp     5501   
> > 6000    .       .       .       abc     Target=M1:501..100 23  I      
> > wormbase        mRNA    5000    6000    +       .       .       .      
> > ID=M7.3 24  M7.3    wormbase        exon    1       300     +       .    
> >   .       M7.3    ID=M7.3.1 25  M7.3    wormbase        exon    301    
> > 400     +       .       .       M7.3    ID=M7.3.2 26  M7.3    wormbase   
> >     exon    401     1000    +       .       .       M7.3    ID=M7.3.3
> >
> > =================================================================
> >
> > I have extended (in an experimental way), the Bio::Tools::GFF module
> > to accomodate this new format.  Here is a test script and its output
> > when run on the above file.
> >
> >   0  #!/usr/bin/perl -w
> >   1  use strict;
> >   2  use lib '.';
> >
> >   3  use Bio::Tools::GFF;
> >   4  my $gffio = Bio::Tools::GFF->new(-fh=>\*STDIN,-gff_version=>3);
> >   5  my @f = $gffio->features;
> >   6  format_features(\@f);
> >
> >   7  sub format_features {
> >   8    my $features = shift;
> >   9    my $tabs     = shift || 0;
> >  10    for my $f (@$features) {
> >  11      my $type  = $f->primary_tag;
> >  12      my $id    = $f->unique_id;
> >  13      $id       ||= '(no id)';
> >  14      my ($start,$end) = ($f->start,$f->end);
> >  15      my $alt = ($f->alternative_locations)[0];
> >  16      my ($target,$tstart,$tend) =
> > ($alt->seq_id,$alt->start,$alt->end) if $alt;
> >
> >  17      print
> > "\t"x$tabs,join("\t",$id,$type,$f->location->to_FTstring,eval{$alt->locat
> >ion->seq_id,$alt->location->to_FTstring}),"\n"; 18     
> > format_features([$f->sub_SeqFeature],$tabs+1);
> >  19    }
> >  20  }
> >
> >  21  1;
> >
> > OUTPUT:
> >
> > cTel33B	clone	1..2679
> > CHROMOSOME_I	contig	1..14972282
> > 12345.s	match	join(101..500,1..100,501..1000)
> > M7.3	mRNA	5000..6000
> > 	M7.3.1	exon	5000..5299
> > 	M7.3.2	exon	5300..5399
> > 	M7.3.3	exon	5400..5999
> > abc	match	5001..6000
> > 	(no id)	hsp	5001..5500
> > 	(no id)	hsp	5501..6000
> > (no id)	repeat	5000..5100
> > Y74C9A.1	gene	43733..44677
> > 	Y74C9A.1a	mRNA	43733..44677
> > 		e1	exon	43733..43961
> > 			(no id)	coding_start	43740
> > 		e2	exon	44030..44234
> > 		e4	exon	44521..44677
> > 			(no id)	coding_end	44677
> > 		(no id)	cds	43740..43961
> > 		(no id)	cds	44030..44234
> > 		(no id)	cds	44521..44677
> > 	Y74C9A.1b	mRNA	43733..44677
> > 		e1	exon	43733..43961
> > 			(no id)	coding_start	43740
> > 		e3	exon	44281..44328

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




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